matplotlib-users Mailing List for matplotlib

Hello list,

I know that this is very simple for most of the people, but since it 
took some time to figure it out I'm sharing here. It's useful for those 
that, like me, have dozens of personalized colormaps in matlab r,g,b lists.


def cmat2cmpl(r, g, b):
     """
     Convert matlab style colormap to matplotlib style
     Enter a list non normalized RGB values from 0-255
     """
     r = np.array(r)/255.
     g = np.array(g)/255.
     b = np.array(b)/255.

     cmap = mpl.colors.ListedColormap(zip(r,g,b))
     return cmap


r = [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 
9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 
10, 10, 10, 10, 11, 11, 10, 9, 8, 8, 7, 6, 5, 5, 4, 3, 2, 2, 1, 0, 0]
g = [241, 237, 234, 231, 228, 225, 222, 218, 215, 212, 209, 204, 199, 
194, 190, 185, 180, 175, 171, 166, 161, 160, 158, 157, 156, 154, 153, 
152, 150, 149, 148, 146, 145, 144, 142, 141, 140, 134, 129, 124, 119, 
114, 109, 103, 98, 93, 88, 83, 77, 72, 67, 62, 57, 51, 46, 41, 36, 31, 
25, 20, 15, 10, 5, 0]
b = [255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 
255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 
255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 
255, 255, 255, 255, 255, 255, 255, 255, 247, 240, 232, 225, 217, 210, 
202, 195, 188, 180, 173, 165, 158, 150, 143]

mycmap = cmat2cmpl(r, g, b)
a=outer(arange(0,1,0.001),ones(10))
imshow(a,aspect='auto',cmap=mycmap,origin="lower")

On 8/13/10 5:04 PM, mat...@li... wrote:
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> Today's Topics:
>
>     1. Re: TeX not working with Matplotlib (Jouni Sepp?nen)
>     2. Screenshot on homepage (Simon Friedberger)
>     3. Re: Screenshot on homepage (Aman Thakral)
>     4. Re: Hints on sizing plot elements? (Russell Owen)
>     5. False empty strings in csv2rec (Sergi Pons Freixes)
>     6. embed matplotlib Figure into Tkinter Canvas (gur...@me...)
>
>
> ----------------------------------------------------------------------
> Message: 1
>
> Date: Thu, 12 Aug 2010 18:49:44 +0000 (UTC)
> From: Jouni Sepp?nen<jk...@ik...>
> Subject: Re: [Matplotlib-users] TeX not working with Matplotlib
> To: mat...@li...
> Message-ID:<loo...@po...>
> Content-Type: text/plain; charset=utf-8
>
> Harry Boer<henriaboer@...>  writes:
>
>> This is e-TeX, Version 3.141592-2.1 (Web2C 7.5.2)
>> This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009)
> These are different versions. Do you have two different TeX distributions
> installed on your computer?
Yes, I did install TeX Live at a later stage thinking that it would 
clean up the earlier version.

>> ~ Harry$ which latex
>> /usr/local/bin/latex
> I think TeX Live installs in /usr/texbin on Mac OS X, although it could make
> symlinks in /usr/local/bin. Perhaps /usr/texbin/latex is the version you want.
OK, but how do I go about this? Where can I set which version to use. I 
have set my PATH to /usr/texbin
in the .bash_profile, .bashrc and .profile (just to make sure), but how 
can I make this my default version for Matplotlib? I did not
see any path variables in the matplotlibrc file and I'm not going to 
tinker with that if I'm not sure.
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 12 Aug 2010 22:44:43 +0200
> From: Simon Friedberger<sim...@a-...>
> Subject: [Matplotlib-users] Screenshot on homepage
> To: mat...@li...
> Message-ID:<201...@a-...>
> Content-Type: text/plain; charset=us-ascii
>
> Hi list members.
>
> Does anybody know how to create the graph in the middle of this
> http://matplotlib.sourceforge.net/_static/logo_sidebar_horiz.png
> image on the homepage. I can't find it in the examples and suspect it
> may have been taken out in a previous revision. Does anybody remember?
>
> Best
> Simon
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 12 Aug 2010 16:57:51 -0400
> From: Aman Thakral<ama...@gm...>
> Subject: Re: [Matplotlib-users] Screenshot on homepage
> To: mat...@li...
> Message-ID:
> 	<AAN...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Simon,
>
> I'm fairly sure its just a contour plot with different color mappings for
> the lines and the fill.
>
> There are several examples of this on the site.
>
> Start here:
> http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.contour
>
> Best of Luck,
> Aman
>
> On Thu, Aug 12, 2010 at 4:44 PM, Simon Friedberger<
> sim...@a-...<simon%2Bm...@a-...>>  wrote:
>
>> Hi list members.
>>
>> Does anybody know how to create the graph in the middle of this
>> http://matplotlib.sourceforge.net/_static/logo_sidebar_horiz.png
>> image on the homepage. I can't find it in the examples and suspect it
>> may have been taken out in a previous revision. Does anybody remember?
>>
>> Best
>> Simon
>>
>>
>> ------------------------------------------------------------------------------
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>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>

Dear John,

thank you for your suggestion.  Unfortunately, I have just tried that and I am positive that it does not work.

It works only if the option "frameon" of the figure is True, which is not what I want in this case (I have to produce a pdf with transparent background).

Regards,
Andrea

On Aug 13, 2010, at 17:21 , John Hunter wrote:

> On Fri, Aug 13, 2010 at 1:42 AM,  <gur...@me...> wrote:
>> Dear All,
>> 
>> I am trying to embed a matplotlib Figure into a Tkinter Canvas.  The problem is, when I change the content of the figure (e.g. I delete and create new axes) the new items are plotted but the old items are not deleted.  The old items disappear immediately when I resize the window.
> 
> Just call fig.canvas.draw() after clearing the old items.  This is
> what the resize is doing.
> 
> JDH

On Thu, Aug 12, 2010 at 8:10 PM, Sergi Pons Freixes <sp...@ut...> wrote:
> Hi everybody,
>
> I have a csv file which I would like to read with pylab.csv2rec . The
> file has a header row, values speparated by commas, and a lot of
> missings as empty entries. So, a line with missings looks like:
> col1,col2,,,,col6 . I tried specifyng the parameter with name
> "missing", so it reads:

Can you post the file, here if it is small, or somewhere like drop.io
if it is large?

Thanks,
JDH

On Fri, Aug 13, 2010 at 1:42 AM,  <gur...@me...> wrote:
> Dear All,
>
> I am trying to embed a matplotlib Figure into a Tkinter Canvas.  The problem is, when I change the content of the figure (e.g. I delete and create new axes) the new items are plotted but the old items are not deleted.  The old items disappear immediately when I resize the window.

Just call fig.canvas.draw() after clearing the old items.  This is
what the resize is doing.

JDH

Dear All,

I am trying to embed a matplotlib Figure into a Tkinter Canvas.  The problem is, when I change the content of the figure (e.g. I delete and create new axes) the new items are plotted but the old items are not deleted.  The old items disappear immediately when I resize the window.

I have checked that the elements of Tkinter do their job: the Canvas that contains my figure properly refreshes itself etc, so this is an issue with matplotlib.  A similar problem happens indeed using matplotlib with pylab from e.g. ipython -- there one solves the problem by calling the method show() of pylab.figure.  In the present case I cannot do that because I have to use matplotlib.figure.Figure instead of matplotlib.figure, and the former lacks the show() method.

I googled a lot for this problem and, while many people discusses refreshing issues, I did not find the solution that I need.  Please find below my short code for reference.  I may be missing understanding of how this FigureCanvasTkAgg function works: as far as I see, it connects the Canvas of Tkinter (that is the widget in the application) to the real matplotlib.figure.Figure that I want to plot.

Any help will be greatly appreciated.

Best regards,
Andrea

################################################################################
# CODE BEGINS
################################################################################
#!/usr/bin/env python

import sys
import numpy as N
import Tkinter
import matplotlib, matplotlib.figure
# Set the backend for matplotlib.
matplotlib.use("TkAgg")
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg

class App:
    def __init__(self,master):

        # Set the properties of the whole window.
        master.config(background="gray")
        master.wm_title("PaperPlot")

        # Create a figure and link it to the Tk canvas.
        self.f = matplotlib.figure.Figure(figsize=(3.46, 2.14), frameon=False, dpi=200)

        # This canvas links the figure to the Tk canvas.
        self.canvas = FigureCanvasTkAgg(self.f, master=master)
        self.canvas._tkcanvas.config(background="#c0c0c0", borderwidth=0, highlightthickness=0)
        self.canvas.draw()

        # The Tk canvas.
        self.tkcanvas = self.canvas.get_tk_widget()
        self.tkcanvas.pack(fill=Tkinter.X)

        # A frame that contains the buttons.
        frame0 = Tkinter.Frame(master)
        frame0.pack(fill=Tkinter.X, pady=3)

        # Buttons.
        self.buttonNew = Tkinter.Button(frame0,width=10,text="New",command=self.newPlot)
        self.buttonNew.pack(side=Tkinter.LEFT)

        self.buttonRun = Tkinter.Button(frame0,width=10,text="Run",command=self.runText)
        self.buttonRun.pack(side=Tkinter.LEFT)
        
        self.buttonQuit = Tkinter.Button(frame0,width=10,text='Quit',command=frame0.quit)
        self.buttonQuit.pack(side=Tkinter.RIGHT)

        self.buttonPrint = Tkinter.Button(frame0,width=10,text="Print",command=self.printPlot)
        self.buttonPrint.pack(side=Tkinter.RIGHT)

        # A frame that contains the source code of the plot.
        frame1 = Tkinter.Frame(master)
        frame1.pack(fill=Tkinter.X)
        
        # Text widget with scrollbar that fills the frame and shows the code.
        self.scrollbar = Tkinter.Scrollbar(frame1)
        self.scrollbar.pack(side=Tkinter.RIGHT, fill=Tkinter.Y)
        self.editor = Tkinter.Text(frame1, wrap=Tkinter.WORD, height=20, background="white", yscrollcommand=self.scrollbar.set)
        self.editor.pack(fill=Tkinter.X)
        self.editor.config(highlightthickness=0)
        self.scrollbar.config(command=self.editor.yview)

        # Load the file with the source code of the plot.
        # theFile = open("plot.py", "r")
        # self.editor.insert(Tkinter.END, theFile.read())
        # theFile.close()

        self.i = 1
        
    def newPlot(self):
        self.f.clear()
	# HERE SOMETHING IS NEEDED TO FORCE THE FIGURE TO REDRAW!
        self.a = self.f.add_axes([0.1*self.i, 0.10*self.i, 0.4, 0.74])
        self.i = self.i + 1
        self.canvas.draw()
                
    def runText(self):
        exec(self.editor.get("0.0", Tkinter.END))
        self.canvas.draw()
       
    def printPlot(self):
        self.f.savefig("plot.png", dpi=300)
        self.f.savefig("plot.pdf")
        theText = self.editor.get("0.0", Tkinter.END)
        theFile = open("plot.py", "w")
        print >> theFile, theText
        theFile.close()


# Create the main window of the program.
root = Tkinter.Tk()

# The window is not resizable.
root.resizable(0,0)

# The object that organizes all the widgets and the data in the program.
app = App(root)

# Start the program.
root.mainloop()

################################################################################
# CODE ENDS
################################################################################

On Aug 12, 2010, at 7:37 AM, Tony S Yu wrote:

> On Aug 12, 2010, at 1:08 AM, Russell E. Owen wrote:
>
>> I'm making a strip chart widget (which I plan to make publicly  
>> available
>> when finished). The basics are working fine, but the automatic  
>> sizing is
>> not doing so well. Strip charts are typically short, and when  
>> suitably
>> short the X axis annotations are partially truncated.
>>
>> So...can I convince the automatic sizer to always show the full X  
>> (time)
>> axis annotations and put all the variable sizing into the data  
>> area? Or
>> do I have to manually set them somehow?
>
> As far as I know, there's nothing to automatically resize the  
> padding around the the axes. (The manual way to do it is to call  
> `fig.subplots_adjust`). I wrote a helper script (attached below) to  
> adjust the layout so that there's a specified amount of padding  
> around the axes.
>
> Unfortunately, this resizer doesn't function correctly when using  
> the GTK backend. It apparently works fine with TkAgg, MacOSX, and  
> Qt4Agg backends.

Fortunately I'm using TkAgg. I'm sorry (though not surprised) I'll  
have to size it manually (especially since users of my application can  
change the font size), but I very much appreciate the code.

> Also, is there a way from my software (not a .matplotlibrc file) to
>> globally make the default background color white for axis annotation
>> areas? Right now the background is gray for annotations and while for
>> plot area and I'd prefer it was all white.
>
> Just set plt.rc('figure', facecolor='w') in your code (assuming  
> you've imported matplotlib.pyplot as plt).

Perfect. Thanks!
>
> <tight_layout.py>
>
> Usage note: Since it sounds like you're not creating subplots, you  
> can just use the `tight_borders` function, instead of the  
> `tight_layout` function; the later requires two redraws while the  
> first requires only one.

Thank you very much for the advice and script!

I do plan to support strip charts stacked atop each other (all using  
the same time range, with tick labels only along the bottom x axis),  
which I suspect will need subplots (unless there is now a better way)  
but so far all I have is multiple lines (including dynamic and static  
-- e.g. to display limits) one one plot.

-- Russell

Hi everybody,

I have a csv file which I would like to read with pylab.csv2rec . The
file has a header row, values speparated by commas, and a lot of
missings as empty entries. So, a line with missings looks like:
col1,col2,,,,col6 . I tried specifyng the parameter with name
"missing", so it reads:

data = pylab.csv2rec("myfile.csv", missing='')

But it returned: ValueError: empty string for float()

I thought that csv2rec didn't like the empty string '', so I replaced
in my original files all the ",," for ",nan,". I also replaced the ","
at the end of files for ",nan". Next I tried:

data = pylab.csv2rec("myfile.csv", missing="nan")

But the same error again:

/usr/lib/python2.6/site-packages/matplotlib/mlab.pyc in csv2rec(fname,
comments, skiprows, checkrows, delimiter, converterd, names, missing,
missingd, use_mrecords)
  2323         if not len(row): continue
  2324         if row[0].startswith(comments): continue
-> 2325         rows.append([func(name, val) for func, name, val in
zip(converters, names, row)])
  2326         rowmasks.append([ismissing(name, val) for name, val in
zip(names, row)])
  2327     fh.close()

/usr/lib/python2.6/site-packages/matplotlib/mlab.pyc in newfunc(name, val)
  2195                 return default
  2196             else:
-> 2197                 return func(val)
  2198         return newfunc
  2199

ValueError: empty string for float()

Next, I tried a manual check for empty strings, being paranoid:

fin = open("myfile.csv")
f = fin.readlines()
fin.close()
for i in range(len(f)):
  ....:     tmp = f[i].split(',')
  ....:     for c in tmp:
  ....:         if c == '':
  ....:             print i

And nothing is printed, so no empty strings. Then I tried
scipy.recfromcsv, and it worked perfectly! OpenOffice also has no
problem with it.

Therefore, it seems that the file is ok, but the csv2rec version from
matplotlib find some inconsistency. Any help? Could it be a bug? (as
the scipy version works flawlessly).



-- 
Sergi Pons Freixes
Ph.D. Student
Marine Technology Unit
Centre Mediterrani d'Investigacions Marines i Ambientals (CMIMA-CSIC)
Pg. Marítim Barceloneta, 37-49
E-08003 Barcelona (Spain)
Ph.  +34 93 230 95 00 (ext. 1510)
Fax. +34 93 230 95 55
sp...@ut...
http://www.utm.csic.es