Matplotlib crashes my GTK program

Community matplotlib-users
1

I've managed to work around the problem by:
  - always allocating the requested size to the various widgets
  - not rotating annotation labels vertically.

This was just by trial and error, but it seems to work now...?

Dave.

···

--
David Snowdon
dave@...2600...
http://www.snowdon.id.au

On 14/05/2009, at 2:12 AM, matplotlib-users-request@lists.sourceforge.net wrote:

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Today's Topics:

  1. Re: contour overlapping (Armin Moser)
  2. Re: Subplots (Matthias Michler)
  3. Re: Subplots (Stefanie L?ck)
  4. Re: Matplotlib crashes my GTK program (Jo?o Lu?s Silva)
  5. Re: contour overlapping (Armin Moser)
  6. Re: contour overlapping (Bala subramanian)

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

Message: 1
Date: Wed, 13 May 2009 14:06:01 +0200
From: Armin Moser <armin.moser@...2495...>
Subject: Re: [Matplotlib-users] contour overlapping
To: Bala subramanian <bala.biophysics@...287...>
Cc: matplotlib-users@lists.sourceforge.net
Message-ID: <4A0AB7A9.3070907@...2495...>
Content-Type: text/plain; charset=ISO-8859-1

Bala subramanian schrieb:

Dear Matthias,

Thank you for the information. Could you please provide me a small example
of such overlapping.

Look at
http://matplotlib.sourceforge.net/examples/pylab_examples/contour_image.html

or any other contour example from this page:
http://matplotlib.sourceforge.net/examples/index.html

Armin

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

Message: 2
Date: Wed, 13 May 2009 14:16:21 +0200
From: Matthias Michler <MatthiasMichler@...361...>
Subject: Re: [Matplotlib-users] Subplots
To: matplotlib-users@lists.sourceforge.net
Message-ID: <200905131416.21942.MatthiasMichler@...361...>
Content-Type: text/plain; charset="utf-8"

Hello Stefanie,

I think the problem is that you try to initialise a subplot with
subplot(112)
which is not possible, because the first to numbers in 112 define the subplot
structure / geometry (here 1 by 1) and the last number give the index of the
subplot.
In general you could use N x M (N rows and M columns) for subplots by
subplot(N,M,index)
where 'index' would be a number between 1 and N * M.

best regards Matthias

On Wednesday 13 May 2009 14:02:57 Stefanie L?ck wrote:

Hello!

I'm trying to draw several plots on after the other in a wxScrolledPanel
but I got the error message:

Traceback (most recent call last):
File "D:\Eigene Datein\Python\current\RNAiscan\Test\sample.py", line 96,
in <m odule>
   frame = MyFrame()
File "D:\Eigene Datein\Python\current\RNAiscan\Test\sample.py", line 56,
in __ init__
   self.plot_data(self.fig)
File "D:\Eigene Datein\Python\current\RNAiscan\Test\sample.py", line 90,
in pl ot_data
   a = figure.add_subplot(id)
File "C:\python25\lib\site-packages\matplotlib\figure.py", line 689, in
add_su bplot
   a = subplot_class_factory(projection_class)(self, *args, **kwargs)
File "C:\python25\lib\site-packages\matplotlib\axes.py", line 7207, in
__init_ _
   raise ValueError( 'Subplot number exceeds total subplots')
ValueError: Subplot number exceeds total subplots

Here's my code:

# -*- coding: latin1 -*-
import sys

import wx
import wx.lib.scrolledpanel as SP
from wx.lib.mixins.listctrl import CheckListCtrlMixin

from matplotlib.backends.backend_wx import FigureCanvasWx
from matplotlib.figure import Figure
import matplotlib.numerix as numpy

from pylab import array, arange, sin, cos, exp, pi, randn, normpdf,
meshgrid, \ convolve

d = {1: (' Contig5535', '230 '), 2: (' Contig5534', '3240 '), 3: (' test',
'574')}

class CheckListCtrl(wx.ListCtrl, CheckListCtrlMixin):
   def __init__(self, parent):
       wx.ListCtrl.__init__(self, parent, -1,
style=wx.LC_REPORT|wx.LC_VRULES|wx.LC_HRULES|wx.LC_SORT_ASCENDING)
CheckListCtrlMixin.__init__(self)
       self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnItemActivated)

   def OnItemActivated(self, evt):
       self.ToggleItem(evt.m_itemIndex)

   def OnCheckItem(self, index, flag):
       data = self.GetItemData(index)
       title = d[data][1]
       if flag:
           what = "checked"
       else:
           what = "unchecked"

class MyFrame(wx.Frame):

   def __init__(self):
       wx.Frame.__init__(self, None, -1, "My Frame", size=(300, 300))
       self.panel = SP.ScrolledPanel(self, -1)

       self.list = CheckListCtrl(self.panel)
       self.list.SetFont(wx.Font(10, wx.SWISS, wx.NORMAL, wx.NORMAL))

       vbox = wx.BoxSizer(wx.VERTICAL)

       self.fig = Figure()
       self.canvas = FigureCanvasWx(self.panel, -1, self.fig)
       self.plot_data(self.fig)
       vbox.Add(self.list,0, wx.EXPAND)
       vbox.Add(self.canvas, 1, wx.LEFT|wx.TOP|wx.GROW)

       self.panel.SetSizer(vbox)
       self.panel.SetAutoLayout(1)
       self.panel.SetupScrolling()

       self.list.InsertColumn(0, "ID")
       self.list.InsertColumn(1, "Nr. of Hits")
       for key, data in d.iteritems():
           index = self.list.InsertStringItem(sys.maxint, data[0])
           self.list.SetStringItem(index, 1, data[1])
           #self.list.SetStringItem(index, 2, data[2])
           self.list.SetItemData(index, key)
       self.list.SetColumnWidth(0, wx.LIST_AUTOSIZE)
       self.list.SetColumnWidth(1, 100)
       self.Show()

   def plot_data(self, figure):
       liste2 = ['Contig5535_range.txtcounts.txt',
'Contig5534_range.txtcounts.txt'] id = 111

       for q in liste2:
           f = open(q, 'r')
           data = f.readlines()
           liste3 = []
           liste4 = []
           for line in data:
               line = line.strip()
               x = line.split(" ")
               liste3.append(int(x[0]))
               liste4.append(int(x[1]))

           a = figure.add_subplot(id)
           a.plot(liste3,liste4)
           id = id + 1

if __name__ == '__main__':
   app = wx.PySimpleApp()
   frame = MyFrame()
   frame.Show(True)
   app.MainLoop()

Has someone an idea how to solve this?
Thank in advance
Stefanie

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

Message: 3
Date: Wed, 13 May 2009 15:14:34 +0200
From: Stefanie L?ck <lueck@...2597...>
Subject: Re: [Matplotlib-users] Subplots
To: "Matthias Michler" <MatthiasMichler@...361...>,
  <matplotlib-users@lists.sourceforge.net>
Message-ID: <009801c9d3cc$c2c3f0e0$1022a8c0@...2598...>
Content-Type: text/plain; format=flowed; charset="UTF-8";
  reply-type=original

Thanks a lot! Problem solved!
Stefanie
----- Original Message -----
From: "Matthias Michler" <MatthiasMichler@...361...>
To: <matplotlib-users@lists.sourceforge.net>
Sent: Wednesday, May 13, 2009 2:16 PM
Subject: Re: [Matplotlib-users] Subplots

Hello Stefanie,

I think the problem is that you try to initialise a subplot with
subplot(112)
which is not possible, because the first to numbers in 112 define the
subplot
structure / geometry (here 1 by 1) and the last number give the index of
the
subplot.
In general you could use N x M (N rows and M columns) for subplots by
subplot(N,M,index)
where 'index' would be a number between 1 and N * M.

best regards Matthias

On Wednesday 13 May 2009 14:02:57 Stefanie L?ck wrote:

Hello!

I'm trying to draw several plots on after the other in a wxScrolledPanel
but I got the error message:

Traceback (most recent call last):
File "D:\Eigene Datein\Python\current\RNAiscan\Test\sample.py", line
96,
in <m odule>
   frame = MyFrame()
File "D:\Eigene Datein\Python\current\RNAiscan\Test\sample.py", line
56,
in __ init__
   self.plot_data(self.fig)
File "D:\Eigene Datein\Python\current\RNAiscan\Test\sample.py", line
90,
in pl ot_data
   a = figure.add_subplot(id)
File "C:\python25\lib\site-packages\matplotlib\figure.py", line 689, in
add_su bplot
   a = subplot_class_factory(projection_class)(self, *args, **kwargs)
File "C:\python25\lib\site-packages\matplotlib\axes.py", line 7207, in
__init_ _
   raise ValueError( 'Subplot number exceeds total subplots')
ValueError: Subplot number exceeds total subplots

Here's my code:

# -*- coding: latin1 -*-
import sys

import wx
import wx.lib.scrolledpanel as SP
from wx.lib.mixins.listctrl import CheckListCtrlMixin

from matplotlib.backends.backend_wx import FigureCanvasWx
from matplotlib.figure import Figure
import matplotlib.numerix as numpy

from pylab import array, arange, sin, cos, exp, pi, randn, normpdf,
meshgrid, \ convolve

d = {1: (' Contig5535', '230 '), 2: (' Contig5534', '3240 '), 3: ('
test',
'574')}

class CheckListCtrl(wx.ListCtrl, CheckListCtrlMixin):
   def __init__(self, parent):
       wx.ListCtrl.__init__(self, parent, -1,
style=wx.LC_REPORT|wx.LC_VRULES|wx.LC_HRULES|wx.LC_SORT_ASCENDING)
CheckListCtrlMixin.__init__(self)
       self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.OnItemActivated)

   def OnItemActivated(self, evt):
       self.ToggleItem(evt.m_itemIndex)

   def OnCheckItem(self, index, flag):
       data = self.GetItemData(index)
       title = d[data][1]
       if flag:
           what = "checked"
       else:
           what = "unchecked"

class MyFrame(wx.Frame):

   def __init__(self):
       wx.Frame.__init__(self, None, -1, "My Frame", size=(300, 300))
       self.panel = SP.ScrolledPanel(self, -1)

       self.list = CheckListCtrl(self.panel)
       self.list.SetFont(wx.Font(10, wx.SWISS, wx.NORMAL, wx.NORMAL))

       vbox = wx.BoxSizer(wx.VERTICAL)

       self.fig = Figure()
       self.canvas = FigureCanvasWx(self.panel, -1, self.fig)
       self.plot_data(self.fig)
       vbox.Add(self.list,0, wx.EXPAND)
       vbox.Add(self.canvas, 1, wx.LEFT|wx.TOP|wx.GROW)

       self.panel.SetSizer(vbox)
       self.panel.SetAutoLayout(1)
       self.panel.SetupScrolling()

       self.list.InsertColumn(0, "ID")
       self.list.InsertColumn(1, "Nr. of Hits")
       for key, data in d.iteritems():
           index = self.list.InsertStringItem(sys.maxint, data[0])
           self.list.SetStringItem(index, 1, data[1])
           #self.list.SetStringItem(index, 2, data[2])
           self.list.SetItemData(index, key)
       self.list.SetColumnWidth(0, wx.LIST_AUTOSIZE)
       self.list.SetColumnWidth(1, 100)
       self.Show()

   def plot_data(self, figure):
       liste2 = ['Contig5535_range.txtcounts.txt',
'Contig5534_range.txtcounts.txt'] id = 111

       for q in liste2:
           f = open(q, 'r')
           data = f.readlines()
           liste3 = []
           liste4 = []
           for line in data:
               line = line.strip()
               x = line.split(" ")
               liste3.append(int(x[0]))
               liste4.append(int(x[1]))

           a = figure.add_subplot(id)
           a.plot(liste3,liste4)
           id = id + 1

if __name__ == '__main__':
   app = wx.PySimpleApp()
   frame = MyFrame()
   frame.Show(True)
   app.MainLoop()

Has someone an idea how to solve this?
Thank in advance
Stefanie

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

Message: 4
Date: Wed, 13 May 2009 14:37:44 +0100
From: Jo?o Lu?s Silva <jsilva@...668...>
Subject: Re: [Matplotlib-users] Matplotlib crashes my GTK program
To: matplotlib-users@lists.sourceforge.net
Message-ID: <gueied$80v$1@...1760...>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

David Snowdon wrote:

Hi all,

This will probably end up being my very silly mistake, but at the
moment, Matplotlib crashes my program with an X error whenever my window
isn't expanded far enough.

For those interested, it is a front-end for the strategy and analysis
software for the Sunswift solar car (http://www.sunswift.com). I attach
a screenshot (when it is expanded to the full screen, and therefore
works) in case it helps.

daves@...2601...:~/projects/sunswift/carsoft/scanalysis$ python -c "import
matplotlib; print matplotlib.__version__"
0.91.2

I read the code you sent. You shouldn't import pylab (neither pyplot?),
although you don't seem to be using it. Maybe the paint_event is firing
when it shouldn't?

Aside from that, my only advice would be to update matplotlib to the
latest version.

JLS

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

Message: 5
Date: Wed, 13 May 2009 17:33:11 +0200
From: Armin Moser <armin.moser@...2495...>
Subject: Re: [Matplotlib-users] contour overlapping
To: Bala subramanian <bala.biophysics@...287...>,
  matplotlib-users@lists.sourceforge.net
Message-ID: <4A0AE837.4050906@...2495...>
Content-Type: text/plain; charset=ISO-8859-1

Bala subramanian schrieb:

hai Armin,

I looked through the examples. I could not find any example of overlapping
two differnet countours on the same plot.

I think the first example filled contours does exactly that. You want to
show two contours over each other in the same plot.
You just have to substitute the Z in cset_1 with matrix_1 and in cset_2
with matrix_2. Of course it will be helpful to use different colormaps.
E.g. a grey one for the underlying contour and a colored for the top one.

x = arange(5)
y = arange(5)
x,y = meshgrid(x,y)
Z = x**2+y**2
#contourf(Z,cmap=cm.binary) # filled contours gray
contour(Z) # not filled contours colored
error = rand(x.shape[0],x.shape[1]) # to generate a new Z
Z = (x+error)**2+(y+error)**2
contour(Z) # colored not filled contours

Armin

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

Message: 6
Date: Wed, 13 May 2009 18:12:53 +0200
From: Bala subramanian <bala.biophysics@...287...>
Subject: Re: [Matplotlib-users] contour overlapping
To: Armin Moser <armin.moser@...2495...>
Cc: matplotlib-users@lists.sourceforge.net
Message-ID:
  <288df32a0905130912w42fe4df3me9874e7df8fe94a7@...288...>
Content-Type: text/plain; charset="iso-8859-1"

Armin,
I tried this but what happens is it is not overlapping, actually when i call
contour function for the second time with matrix2, the plot is updated with
contour of matrix 2.

contour(matrix1)
contour(matrix2).

What i finally get is the contour of matrix 2 as the final plot. What i am
trying to do is that, i shd have one plot, with upper left panel for matrix1
and lower right panel for matrix2 with their separation along the diagonal.
I have attached an example picture like which i am trying to make.

Bala

On Wed, May 13, 2009 at 5:33 PM, Armin Moser > <armin.moser@...2495...>wrote:

Bala subramanian schrieb:

hai Armin,

I looked through the examples. I could not find any example of

overlapping

two differnet countours on the same plot.

I think the first example filled contours does exactly that. You want to
show two contours over each other in the same plot.
You just have to substitute the Z in cset_1 with matrix_1 and in cset_2
with matrix_2. Of course it will be helpful to use different colormaps.
E.g. a grey one for the underlying contour and a colored for the top one.

x = arange(5)
y = arange(5)
x,y = meshgrid(x,y)
Z = x**2+y**2
#contourf(Z,cmap=cm.binary) # filled contours gray
contour(Z) # not filled contours colored
error = rand(x.shape[0],x.shape[1]) # to generate a new Z
Z = (x+error)**2+(y+error)**2
contour(Z) # colored not filled contours

Armin

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