Nabble - matplotlib - users

Re: animated axis

2009-12-04T14:20:13Z

avee wrote:

Dear users,
I have been working on a scope based on matplotlib to monitor acquisition data. In order to enhance frame per seconds, I have used matplotlib's blit capabilities and works ok. No flickering, nice and smooth. Here's how it's done, take note that bbox is taken from the figure and not the axes object in order to make the scale animated. The problem I have, is that the figure is all white because of this.. just a question of esthetics :-) If bbox is taken from the axis, the scale will never be drawn. Any suggestion?

This worked for me:
to remove axis temporary and than to take background of the whole picture but without ticks and labels of this axis:

self.axxaxis = self.ax.get_xaxis()

# store ticker
MJF = self.axxaxis.get_major_formatter()
MJL = self.axxaxis.get_major_locator()
#remove axis
self.axxaxis.set_major_formatter(NullFormatter())
self.axxaxis.set_major_locator(NullLocator())

self.draw()

...
take background for blit
...

# restore ticker
self.axxaxis.set_major_formatter(MJF)
self.axxaxis.set_major_locator(MJL)

Re: AxesGrid problem.

2009-12-04T13:07:49Z

On Fri, Dec 4, 2009 at 2:49 PM, Ryan Neve <ryan.neve@...> wrote:

Than you for your assistance with AxesGrid.

Concerning the documentation, on this page:http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.htm it says:

Name Default Description

aspect True aspect of axes

then a few lines below:
"aspect
By default (False), widths and heigths of axes in the grid are scaled independently. If True, they are scaled according to their data limits (similar to aspect parameter in mpl)."

Thanks a lot.

This need to be fixed.

Here is a more complete example of my code:
In the following code, x_grid and y_grid are are arrays created by meshgrid and represent time and water depth respectively.
z_dim is a dictionary of one or more arrays of sensor readings corresponding to the depths and times in x_grid and y_grid.

Please, "more" complete example does not make any difference unless it is complete.

Try the following code. This is based on the first part of your example. It will show empty axes but without extra ticklabels. Again, I think an extra axes is added to the figure somewhere in your code. And, without a complete, runnable (but simple) code, there is not much I (or others) can help.

-JJ

from matplotlib import pyplot

from mpl_toolkits.axes_grid import AxesGrid

nrows = 3

DAP_figure = pyplot.figure(1,(20,8))

pyplot.figtext(0.05,.5,"Depth (m)",rotation='vertical',verticalalignment='center')

# Create a grid of axes with the AxesGrid helper class

my_grid = AxesGrid(DAP_figure, 111, # Only one grid in this figure

nrows_ncols = (nrows,1), # one or more rows, but only one column

axes_pad = 0.0, #pad between axes in inches

aspect=False, # If True, all plots are superimposed upon one another.

add_all=True, # not sure why this would ever be False

share_all=True, # I think this means that all axes have the same x & y scales

label_mode = "L", # labels for depth on left and time on bottom

cbar_location="right",

cbar_mode="each", # each axes has a different scale

cbar_size="2%",

cbar_pad="1%",

)

pyplot.draw()

pyplot.show()

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Re: Rotating X-Labels on AxesGrid?

2009-12-04T12:09:14Z

First of all, unless you're displaying multiple images (with aspect),
there is not much of benefit of using axes_grid toolkit. So I
strongly recommend you to stick to subplot.

axes_grid toolkit uses different kind of artists to draw ticklabels.
Therefore, most of the matplotlib command that try to change the
properties of the ticklabels does not work.

http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html

http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/axislines.html

You may recover the original matplotlib behavior, but some of the
feature in axes_grid toolkit won't work.

http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#axisline

axes_grid way of rotating ticklabels is

ax.axis["bottom"].major_ticklabels.set_rotation(90)

But, you may want to fiddle with other properties also.

ax.axis["bottom"].major_ticklabels.set_va("top")
ax.axis["bottom"].major_tick_pad = -8

Anyhow, I must admit that handling of ticklabels in axes_grid toolkit
is a bit messy currently. And I hope to improve it soon.

Regards,

-JJ

On Fri, Dec 4, 2009 at 12:56 PM, <PHobson@...> wrote:

> Hey folks,
>
> I'm trying to make some bar plots using AxesGrid and the set_xlabels method doesn't seem to notice that I'm passing a 'rotation' kwarg.
>
> Here's a small script that showing that this doesn't work:
> # ------------------------------------------
> import matplotlib.pyplot as pl
> from mpl_toolkits.axes_grid import AxesGrid
>
> fig = pl.figure()
> grid = AxesGrid(fig, 111, nrows_ncols=(1,1), axes_pad=0.12)
> xlabs = ['paul', 'chris', 'patti']
>
> for ax in grid:
> ax.plot([1,2,3], [2,2.5,3], 'bo')
> ax.set_ylim([0,5])
> ax.set_xlim([0,4])
> ax.set_xticks([1,2,3])
> ax.set_xticklabels(xlabs, rotation=90)
> # -----------------------------------------
>
> As you can see from the attached image, my labels aren't rotating. This is obviously a trivial example, but I'm trying to plot some chemical concentrations and the names are quite long.
>
> Any tips? Should I just be using subpolot instead?
>
> Python 2.6.2 and:
> In [25]: import matplotlib as mpl
> In [26]: mpl.__version__
> Out[26]: '0.99.1'
> In [27]: import numpy as np
> In [28]: np.__version__
> Out[28]: '1.3.0'
>
> Thanks!
>
> Paul M. Hobson
> Senior Staff Engineer
> --
> Geosyntec Consultants
> 55 SW Yamhill St, Ste 200
> Portland, OR 97204
> Phone: (503) 222-9518
> www.geosyntec.com
>
>
>
> ------------------------------------------------------------------------------
> Join us December 9, 2009 for the Red Hat Virtual Experience,
> a free event focused on virtualization and cloud computing.
> Attend in-depth sessions from your desk. Your couch. Anywhere.
> http://p.sf.net/sfu/redhat-sfdev2dev
> _______________________________________________
> Matplotlib-users mailing list
> Matplotlib-users@...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

legend with

2009-12-04T12:07:22Z

I am trying to plot a line area graph similar to a stacked bar chart.

E.g
import matplotlib.pyplot as plt
import numpy as np
fig = plt.figure()
ax = fig.add_subplot(111)
ind = np.arange(3)
y1 = np.array([1,2,3])
y2 = y1 * 2
a = ax.fill_between(ind, y1, np.zeros(len(ind)), facecolor='r')
b = ax.fill_between(ind, y2, y1, facecolor='b')
plt.show()

However, when I try to make my legend,

ax.legend((a,b),('a','b'))

I get an AttributeError. How do I extract the information I need from the PolyCollection object to make a legend?
Thanks,

- Chuck

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Re: AxesGrid problem.

2009-12-04T11:49:46Z

Than you for your assistance with AxesGrid.

Concerning the documentation, on this page:http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.htm it says:

Name	Default	Description
aspect	True	aspect of axes

then a few lines below:
"aspect

By default (False), widths and heigths of axes in the grid are scaled independently. If True, they are scaled according to their data limits (similar to aspect parameter in mpl)."

Here is a more complete example of my code:
In the following code, x_grid and y_grid are are arrays created by meshgrid and represent time and water depth respectively.
z_dim is a dictionary of one or more arrays of sensor readings corresponding to the depths and times in x_grid and y_grid.

from matplotlib import pyplot
from mpl_toolkits.axes_grid import AxesGrid
nrows = len(z_dim) # Number of rows
DAP_figure = pyplot.figure(1,(20,8))
pyplot.figtext(0.05,.5,"Depth (m)",rotation='vertical',verticalalignment='center')
# Create a grid of axes with the AxesGrid helper class
my_grid = AxesGrid(DAP_figure, 111, # Only one grid in this figure
                nrows_ncols = (nrows,1), # one or more rows, but only one column
                axes_pad = 0.0, #pad between axes in inches
                aspect=False, # If True, all plots are superimposed upon one another.
                add_all=True, # not sure why this would ever be False
                share_all=True, # I think this means that all axes have the same x & y scales
                label_mode = "L", # labels for depth on left and time on bottom
                cbar_location="right",
                cbar_mode="each", # each axes has a different scale
                cbar_size="2%",
                cbar_pad="1%",
                )

for i,parameter in enumerate(z_dim):
    z_dim[parameter] = maskDAP(z_dim[parameter],parameter,dev_mult) #Need to mask NaNs and outliers for each grid
    ax = my_grid[i].pcolor(x_grid,y_grid,z_dim[parameter])
    my_grid[i].set_ylabel(long_name[parameter]) # Puts a y label on every graph.
    my_grid.cbar_axes[i].colorbar(ax)
    my_grid.cbar_axes[i].axis["right"].toggle(ticklabels=True,label=True)
    my_grid.cbar_axes[i].set_ylabel(units[parameter]) #Puts the units on the right side of the colorbar
pyplot.draw()
pyplot.show()

I do need a separate colorbar for each plot as they are results of different sensors all taken at the same time and depth scales.
Here is what I have now:

Which, aside from the extra scale labels on the x and y axis is getting close.

Thank You for your help,

-Ryan

matplotlib version:

On Thu, Dec 3, 2009 at 4:36 PM, Jae-Joon Lee <lee.j.joon@...> wrote:

On Thu, Dec 3, 2009 at 3:40 PM, Ryan Neve <ryan.neve@...> wrote:

I tried all sorts of things, but finally, by setting aspect=False I got it to work. In the documentation, the table says this defaults to True and the explanation of aspect below says it defaults to False. Although I don't entirely understand what is going on, I think this threw me off.
So then I had this:

Can you be more specific about which documentation says the default aspect is False? This may need to be fixed. Note that AxesGrid is designed for displaying images with aspect=True. Otherwise, you may better stick to the subplot..

... which looks much better, except that there are two sets of x and y axis labels? This seems to have something to do with the colorbar. I've got:

To me, there is another axes underneath the AxesGrid. It is hard to tell without a complete code.

                    label_mode = "L",
                    cbar_location="right",
                    cbar_mode="each",

                    cbar_size="2%",
                    cbar_pad="0.5%"

Now I'm trying to get scales and labels on my colorbars.
I tried:
for i,parameter in enumerate(z_dim):
    ax = my_grid[i].pcolor(x_grid,y_grid,z_dim[parameter]) # This is the pcolor plot
    my_grid[i].set_ylabel('Depth') # Correctly puts a y label on every plot.
    cb = my_grid.cbar_axes[i].colorbar(ax) # Puts in a colorbar for this axes?s
    cb.set_ylabel(parameter) #It would be nice if this was on the far right next to the colorbar. I don't see it anywhere. Perhaps underneath something?

The label of the colorbar is set to invisible by default (this is a bug). So, try something like

   my_grid.cbar_axes[i].set_ylabel(parameter)
   my_grid.cbar_axes[i].axis["right"].toggle(ticklabels=True,

   label=True)

It looks like perhaps the colorbar axes is inside the ax axes rather than besides it?
In the demo_grid_with_each_cbar example, how would you put a scale and label on the colorbar like in this plot:?

I can put a y_label on each contour plot, but since they all have depth, I'd like to label this only once.
Is there a way to label the entire AxesGrid (or is that subplot?)?

Does label_mode="1" do what you want?
You may manually make some of the labels invisible.

Please post a "complete", but simple, script that reproduces your problem. Otherwise, it is hard to track down what is wrong.

Also, please report what version of matplotlib you're using. The axes_grid toolkit is relatively new and some of the feature may not work in older versions.

Regards,

-JJ

Thank you very much for your help,

-Ryan

On Wed, Dec 2, 2009 at 10:21 PM, Jae-Joon Lee <lee.j.joon@...> wrote:

This happens because, when the AxesGrid is created, gca() is set to the last axes, which is the last colobar axes.

If you use axes_grid toolkit, you'd better not use pyplot command that works on axes. Instead, use axes method directly.

For example, instead of "pyplot.pcolor(..)" , use "ax.pcolor(..)".

Regards,

-JJ

On Wed, Dec 2, 2009 at 2:18 PM, Ryan Neve <ryan.neve@...> wrote:

Hello,

I'm trying to use AxesGrid but I'm running into a problem:
I can plot a single pcolor plot:

But when I try to use AxesGrid, my pcolor plot is ending up where I expect my colorbar to be.

I want to have up to 6 of these plots stacked vertically, sharing a common time axis and y (depth) scale.

I'll try to simplify my code to show what I'm doing:

# I have arrays x_grid and y_grid for time and water depth.
# z_dim is a dictionary of arrays (one for each plot)
# In the plot above it has two arrays.
from matplotlib import pyplot
nrows = len(z_dim) # Number of rows is the number of arrays
My_figure = pyplot.figure(1,(8,8))
my_grid = AxesGrid(My_figure, 111, #Is this always 111?
                nrows_ncols = (nrows,1), # Always one column
                axes_pad = 0.1,
                add_all=True,
                share_all=True, # They all share the same time and depth scales
                label_mode = "L",
                cbar_location="right",
                cbar_mode="each",
                cbar_size="7%",
                cbar_pad="2%",
                )
for row_no,parameter in enumerate(z_dim):
    ax = my_grid[row_no]
    ax = pyplot.pcolor(x_grid,y_grid,z_dim[parameter])
pyplot.draw()
pyplot.show()

I eventually want to end up with something like this matlab output (which I didn't generate):

but without the duplication of x scales.

I'm new to pyplot and even after reading the documentation much of this is baffling.

-Ryan

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Matplotlib - navigation toolbar - delete x and y labelling

2009-12-04T10:57:39Z

Hi all,

I'd like to delete x and y labelling in the navigation toolbar.

See picture: http://img256.imageshack.us/img256/1608/capturepc.th.png

How can I do this ?

Thanks for your answer

Rotating X-Labels on AxesGrid?

2009-12-04T09:56:51Z

Hey folks,

I'm trying to make some bar plots using AxesGrid and the set_xlabels method doesn't seem to notice that I'm passing a 'rotation' kwarg.

Here's a small script that showing that this doesn't work:
# ------------------------------------------
import matplotlib.pyplot as pl
from mpl_toolkits.axes_grid import AxesGrid

fig = pl.figure()
grid = AxesGrid(fig, 111, nrows_ncols=(1,1), axes_pad=0.12)
xlabs = ['paul', 'chris', 'patti']

for ax in grid:
ax.plot([1,2,3], [2,2.5,3], 'bo')
ax.set_ylim([0,5])
ax.set_xlim([0,4])
ax.set_xticks([1,2,3])
ax.set_xticklabels(xlabs, rotation=90)
# -----------------------------------------

As you can see from the attached image, my labels aren't rotating. This is obviously a trivial example, but I'm trying to plot some chemical concentrations and the names are quite long.

Any tips? Should I just be using subpolot instead?

Python 2.6.2 and:
In [25]: import matplotlib as mpl
In [26]: mpl.__version__
Out[26]: '0.99.1'
In [27]: import numpy as np
In [28]: np.__version__
Out[28]: '1.3.0'

Thanks!

Paul M. Hobson
Senior Staff Engineer
--
Geosyntec Consultants
55 SW Yamhill St, Ste 200
Portland, OR 97204
Phone: (503) 222-9518
www.geosyntec.com

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rotate_test.png (30K) Download Attachment

Unable to plot simple matplotlib figures

2009-12-04T08:20:22Z

Hello.

I installed matplotlib from source in Mac OS 10.6. However, I am
unable to print this simple example plot:
from pylab import *
plot([1,2,3])
show()

Here is what I get when I try using TkAgg as the backend:

casa98-125-dhcp:.matplotlib lisa$ python simple_plot.py --verbose-
helpful
$HOME=/Users/lisa
matplotlib data path /Users/lisa/.local/lib/python2.6/site-packages/
matplotlib/mpl-data
loaded rc file /Users/lisa/.matplotlib/matplotlibrc
matplotlib version 0.99.1.1
verbose.level helpful
interactive is True
units is False
platform is darwin
CONFIGDIR=/Users/lisa/.matplotlib
Using fontManager instance from /Users/lisa/.matplotlib/fontList.cache
backend TkAgg version 8.5
Traceback (most recent call last):
File "simple_plot.py", line 2, in <module>
plot([1,2,3])
File "/Users/lisa/.local/lib/python2.6/site-packages/matplotlib/
pyplot.py", line 2134, in plot
ax = gca()
File "/Users/lisa/.local/lib/python2.6/site-packages/matplotlib/
pyplot.py", line 582, in gca
ax = gcf().gca(**kwargs)
File "/Users/lisa/.local/lib/python2.6/site-packages/matplotlib/
pyplot.py", line 276, in gcf
return figure()
File "/Users/lisa/.local/lib/python2.6/site-packages/matplotlib/
pyplot.py", line 254, in figure
**kwargs)
File "/Users/lisa/.local/lib/python2.6/site-packages/matplotlib/
backends/backend_tkagg.py", line 91, in new_figure_manager
canvas = FigureCanvasTkAgg(figure, master=window)
File "/Users/lisa/.local/lib/python2.6/site-packages/matplotlib/
backends/backend_tkagg.py", line 158, in __init__
master=self._tkcanvas, width=w, height=h)
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/lib-tk/Tkinter.py", line 3284, in __init__
Image.__init__(self, 'photo', name, cnf, master, **kw)
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/lib-tk/Tkinter.py", line 3240, in __init__
self.tk.call(('image', 'create', imgtype, name,) + options)
_tkinter.TclError: integer value too large to represent

I've tried the MacOSX backend and that opens a GUI that has the label
Figure 1 but no plot. Saving to a post script file does not work
either. Does anyone know what the problem is?

Lisa

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Re: Publish to HTML

2009-12-04T06:07:22Z

Another possibility is pyReport:
http://gael-varoquaux.info/computers/pyreport/

Alan Isaac

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Beginner Problem with drawing

2009-12-04T06:01:54Z

Hi guys,

i wrote a little program to display filter sets used for microscopy. The spectra data are shown using matplotlib and wxmpl. The GUI hat a menu item "Set Lines" --> an extra Frame with checkboxes will open up.
Upon checking or unchecking, the laser lines should be displayed or deleted inside the main panel as vertical lines, but I juts can not figure out, how to acess the meain panel when checking.

The problem is located in line 58, 63 and 68

Here is the code:

#!/usr/bin/env python

import numpy
from pylab import *
import scipy
import scipy.linalg
import wx
import wxmpl
import os, sys

xmin = 350
xmax = 700
ymin = 0
ymax = 1.05

# normalizes dye spectra to 1
def normspec(datain):
        out = datain
        out[:,1] = datain[:,1]/datain[:,1].max(0)
        return out

# converts filters spectra to 0-1 range
def normspec_filter(datain):
        out = datain
        if datain[:,1].max(0)>10:
            out[:,1] = datain[:,1]/100
        return out

class MyApp(wx.App):
    def OnInit(self):
        self.frame = MyFrame(None, -1, 'FilterSpectra')
        self.frame.Show(True)
        return True

class SetLaser(wx.Frame):
    def __init__(self, parent, id, title):
        wx.Frame.__init__(self, parent, id, title, size=(220, 130))

        wl = array([405, 445, 473])
        panel = wx.Panel(self, -1)

        self.cb0 = wx.CheckBox(panel, 10, str(wl[0])+'nm', (10, 10))
        self.cb1 = wx.CheckBox(panel, 11, str(wl[1])+'nm', (80, 10))
        self.cb2 = wx.CheckBox(panel, 12, str(wl[2])+'nm', (150, 10))

        self.Bind(wx.EVT_CHECKBOX, self.on_checkbox0, id=10)
        self.Bind(wx.EVT_CHECKBOX, self.on_checkbox1, id=11)
        self.Bind(wx.EVT_CHECKBOX, self.on_checkbox2, id=12)

        self.CenterOnParent()
        self.Show()

    def on_checkbox0(self, event):
            self.cb0value = event.IsChecked()
            print self.cb0value
            self.glaser0, = self.axes.plot([wl[i],wl[i]],[0,1],'b', lw=2)

    def on_checkbox1(self, event):
            self.cb1value = event.IsChecked()
            print self.cb1value
            self.glaser1, = self.axes.plot([wl[i],wl[i]],[0,1],'b', lw=2)

    def on_checkbox2(self, event):
            self.cb2value = event.IsChecked()
            print self.cb2value
            self.glaser2, = self.axes.plot([wl[i],wl[i]],[0,1],'b', lw=2)

class MyFrame(wx.Frame):
    def __init__(self, parent, id, title):
        wx.Frame.__init__(self, parent, id, title, size=(1000, 800))

        menuBar = wx.MenuBar()
        self.CreateStatusBar()
        #--------------------------------------------------------------
        file = wx.Menu()
        file.Append(100, 'Save As ...', 'Saves Figure as ...')
        file.AppendSeparator()
        file.Append(113, '&Quit\tCtrl+W')
        #--------------------------------------------------------------
        dyes = wx.Menu()
        dyes.Append(101, '&Load Dye Absorption', 'Loads Absorption Spectra (*.abs)')
        dyes.Append(102, '&Load Dye Fluorescence', 'Loads Fluorescence Emission Spectra (*.flu)')
        dyes.AppendSeparator()
        dyes.Append(111, '&Delete last Absorption', 'Deletes last Absorption Spectra')
        dyes.Append(112, '&Delete last Fluorescence', 'Deletes last Fluorescence Emission')
        #--------------------------------------------------------------

        filter = wx.Menu()
        filter.Append(103, '&Load Excitation Filter', 'Loads Excitation Filter (*.ex)')
        filter.Append(104, '&Load Dichroic Mirror', 'Loads Dichroic Mirror (*.di)')
        filter.Append(105, '&Load Emission Filter', 'Loads Emission Filter (*.em)')
        filter.AppendSeparator()
        filter.Append(107, '&Delete last EX filter', 'Deletes the last EX filter')
        filter.Append(108, '&Delete last DI mirror', 'Deletes the last DI mirror')
        filter.Append(109, '&Delete last EM filter', 'Deletes the last EM filter')
        #--------------------------------------------------------------
        lightsource = wx.Menu()
        lightsource.Append(106, '&Load Light Source', 'Loads Spectral Data of Light Source (*.txt)')
        lightsource.AppendSeparator()
        lightsource.Append(110, '&Delete last Light Source', 'Deletes the last Light Source')
        #--------------------------------------------------------------
        laserline = wx.Menu()
        laserline.Append(114, '&Set Laser Lines',' Displays the selected laser lines')
        #--------------------------------------------------------------
        menuBar.Append(file, '&File')
        menuBar.Append(dyes, '&Dyes')
        menuBar.Append(filter, '&Filter')
        menuBar.Append(lightsource, '&Light Source')
        menuBar.Append(laserline, '&Laser Lines')
        #--------------------------------------------------------------
        self.SetMenuBar(menuBar)
        #--------------------------------------------------------------
        self.Bind(wx.EVT_MENU, self.saveas,        id = 100)
        self.Bind(wx.EVT_MENU, self.openabs,    id = 101)
        self.Bind(wx.EVT_MENU, self.openflu,    id = 102)
        self.Bind(wx.EVT_MENU, self.openex,        id = 103)
        self.Bind(wx.EVT_MENU, self.opendi,        id = 104)
        self.Bind(wx.EVT_MENU, self.openem,        id = 105)
        self.Bind(wx.EVT_MENU, self.openls,        id = 106)
        self.Bind(wx.EVT_MENU, self.delex,        id = 107)
        self.Bind(wx.EVT_MENU, self.deldi,        id = 108)
        self.Bind(wx.EVT_MENU, self.delem,        id = 109)
        self.Bind(wx.EVT_MENU, self.dells,        id = 110)
        self.Bind(wx.EVT_MENU, self.delabs,        id = 111)
        self.Bind(wx.EVT_MENU, self.delflu,        id = 112)
        self.Bind(wx.EVT_MENU, self.OnQuit,        id = 113)
        self.Bind(wx.EVT_MENU, self.laserlines,    id = 114)

        self.plotPanel = wxmpl.PlotPanel(self, -1,)
        fig = self.plotPanel.get_figure()
        self.axes = fig.gca()
        self.axes.set_xticks(arange(xmin - 100, xmax + 100, 25))
        self.axes.set_yticks(arange(ymin - 100, ymax + 100, 0.1));
        self.axes.axis([xmin,xmax,ymin,ymax])
        self.axes.grid(True)
        self.axes.set_xlabel('Wavelength [nm]',fontsize=16)
        self.axes.set_ylabel('Transmission [%] or Intensity [a.u.]',fontsize=16)


    def openex(self, event):
        dlg = wx.FileDialog(self, "Choose a Excitation Filter", os.getcwd(), "", "*.ex*", wx.OPEN)
        if dlg.ShowModal() == wx.ID_OK:
            pathex = dlg.GetPath()
            mypathex = os.path.basename(pathex)
            self.SetStatusText("Selected EX: %s" % mypathex)
            ex = numpy.loadtxt(pathex)
            ex = normspec_filter(ex)
            self.gex, = self.axes.plot(ex[:,0],ex[:,1],'b', lw=2,label = mypathex)
            #self.axes.plot(ex[:,0],ex[:,1],'b', lw=2,label = mypathex)
            self.axes.axis([xmin,xmax,ymin,ymax])
            self.axes.legend(loc=4)
            self.plotPanel.draw()

        dlg.Destroy()
#...
# --> here is some more code ...
#...
class MyApp(wx.App):
    def OnInit(self):
        myframe = MyFrame(None, -1, "FilterSpectra")
        myframe.CenterOnScreen()
        myframe.Show(True)
        return True


app = MyApp(0)
app.MainLoop()

--
Dr. Sebastian Rhode
Grünwalder Str. 103a
81547 München
Tel: +49 89 4703091
sebrhode@...

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Re: Publish to HTML

2009-12-04T05:45:27Z

On 12/4/2009 2:17 AM, David Arnold wrote:
> I am wondering if Sampledoc type files can be used for this same
> purpose. Is there a way you can gather the output html and upload them
> to our Sakai drop boxes?
>

Is the following at all related to what you want to do?
Using reStructuredText, you can use the `include` directive
to include code files, and the `figure` directive to include
figures. The code is actually in the file produced with the
rst2html script; the figures remain in separate files.

Alan Isaac

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Re: Publish to HTML

2009-12-04T05:33:10Z

On Fri, Dec 4, 2009 at 1:17 AM, David Arnold <dwarnold45@...> wrote:

> All.
>
> I see the Sphinx tutorial Sampledoc on the Matplotlib site and am
> working through the tutorial. This semester, my students have really
> enjoyed using Matlab's publish to HTML tool, then they upload the
> resulting files to their Drop Box on our Sakai course management system.
>
> I am wondering if Sampledoc type files can be used for this same
> purpose. Is there a way you can gather the output html and upload them
> to our Sakai drop boxes?

I'm not familiar with the Sakai drop interface, but you can certainly
upload the files generated by Sphinx in _build/html to a web site.
There are normally a bunch of files that need to be uploaded, so it
would help if Sakai supports some kind of directory or zipfile upload.

JDH

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animated axis

2009-12-04T03:37:23Z

Dear users,
I have been working on a scope based on matplotlib to monitor acquisition data. In order to enhance frame per seconds, I have used matplotlib's blit capabilities and works ok. No flickering, nice and smooth. Here's how it's done, take note that bbox is taken from the figure and not the axes object in order to make the scale animated. The problem I have, is that the figure is all white because of this.. just a question of esthetics :-) If bbox is taken from the axis, the scale will never be drawn. Any suggestion?

# Set all the animated object to animated
self.ax.get_xaxis().set_animated(True)
line = Line2D(tdata,ydata,animated=True)

# Then a copy of the display
background = self.canvas.copy_from_bbox(self.fig.bbox)

# then loop over the acquisition and update
self.ax.set_xlim(tdata[-1] - self.maxt,tdata[-1]) # update axis
self.line.set_data(tdata,ydata) # update line data

self.canvas.restore_region(background) # restore background

self.ax.draw_artist(self.line[0]) # redraw line
self.ax.draw_artist(self.ax.get_xaxis()) # redraw axis

self.canvas.blit(self.fig.bbox) # blit

Re: Computing Simple Statistics from a Histogram

2009-12-04T01:58:47Z

Hi, actually, more question was more informational than how to do it. I
wrote a function to do it, but wondered why such a function didn't seem
to exist. In my case, the histogram is from a small processor that
produces frequency data from 307K points. Unraveling the frequency data
and returning it to original set of points seems counterproductive. The
data is produced from the pixel values in a 640x480 image.

Matthias Michler wrote:

> Hi Wayne,
>
> you are right all these function use the sample-data and not the pdf /
> frequency of occurence-histogram, because typically the data is available and
> not the pdf. Maybe the scipy mailing list could give you a solution to your
> problem.
>
> In case that your freqency of occurence are integers you could do something
> like the following to generate the sample-data and than you the previous
> mentioned functions:
> bin_centers = np.array([ 1., 2., 3., 4., 5.])
> n_vals = np.array([1, 3, 0, 2, 1])
> sample_new = np.array([])
> for bin_center, n in zip(bin_centers, n_vals):
> # append new value 'n' times:
> sample_new = np.concatenate((sample_new, [bin_center]*n))
>
> Kind regards,
> Matthias
>
> On Tuesday 01 December 2009 17:51:31 Wayne Watson wrote:
>
>> I do not believe that any of those calculations are based on the pdf,
>> frequency of occurrence-histogram. This, (1, 2,2, 4, 2,5,4) and not this
>> (1,3, 0,2,1). The latter are the frequencies of occurrence for 1,2,3,4,5.
>>
>> John Hunter wrote:
>>
>>> On Tue, Dec 1, 2009 at 6:32 AM, Wayne Watson
>>>
>>> <sierra_mtnview@...> wrote:
>>>
>>>> Is there some statistics function that computes the mean, std. dev.,
>>>> min/max, etc. from a frequency distribution?
>>>>
>>> numpy has many functions for basic descriptive statistics. If "data"
>>> is an array of your data, you can do (import numpy as np)
>>>
>>> mean: np.mean(data)
>>> median: np.median(data)
>>> standard deviation: np.std(data)
>>> min: np.min(data)
>>> max: np.max(data)
>>>
>>> In scipy.stats, there are many more (skew, kurtosis, etc...) See
>>> also, this example:
>>>
>>>
>>> http://matplotlib.svn.sourceforge.net/viewvc/matplotlib/trunk/py4science/
>>> examples/stats_descriptives.py?view=markup&pathrev=4027
>>>
>>> JDH
>>>
>
>
>
> ------------------------------------------------------------------------------
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> a free event focused on virtualization and cloud computing.
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>
>

--
Wayne Watson (Watson Adventures, Prop., Nevada City, CA)

(121.015 Deg. W, 39.262 Deg. N) GMT-8 hr std. time)
Obz Site: 39° 15' 7" N, 121° 2' 32" W, 2700 feet

The popular press and many authorities believe the number
of pedofiles that prowl the web is 50,00. There are no
figures that support this. The number of children below
18 years of age kidnapped by strangers is 1 in 600,000,
or 115 per year. -- The Science of Fear by D. Gardner

Web Page: <www.speckledwithstars.net/>

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Publish to HTML

2009-12-03T23:17:30Z

All.

I see the Sphinx tutorial Sampledoc on the Matplotlib site and am
working through the tutorial. This semester, my students have really
enjoyed using Matlab's publish to HTML tool, then they upload the
resulting files to their Drop Box on our Sakai course management system.

I am wondering if Sampledoc type files can be used for this same
purpose. Is there a way you can gather the output html and upload them
to our Sakai drop boxes?

David Arnold
College of the Redwoods

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Re: How to display axis numbers inside the figure area

2009-12-03T14:23:46Z

Matthias,

And I saw your code now :) and it pretty much looks like mine, with some more or less formatting. Attached is one of my figures where you can see my result!

Re: How to display axis numbers inside the figure area

2009-12-03T14:16:18Z

Matthias,

Thanks for answering. I already solved my problem. I found that there is no function to display on grids the value of the axis (bad when you need to display lat, longitude)... so I made it myself using the text() function and using yticks() and xticks() along with all the formatting properties, all inside of the text function...

Its pretty nice now,
Angelica.

Re: Plotting curves filled with nonuniform color patch

2009-12-03T13:46:33Z

On Dec 3, 2009, at 3:58 PM, Jae-Joon Lee wrote:

> line 1486 of _backend_agg.cpp says
>
> /* TODO: Support clip paths */
>
> So, it seems that, apparently, clipping with arbitrary path has not
> been implemented yet for gouraud shading (pcolormesh will be properly
> clipped if shading is not used).
> I hope Michael pick this up some time soon.
>
> Meanwhile, you may open a feature request ticket on this.
>
> Regards,
>
> -JJ

Hey Jae-Joon,

Thanks for digging into this. Feature request added.

By the way, I was looking through the feature requests and noticed an open feature request (ID: 2112292) that was satisfied by the addition of spines in the last major release. Just an FYI, if someone with privileges wants to close the request.

Thanks,
-Tony
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Re: AxesGrid problem.

2009-12-03T13:36:23Z

On Thu, Dec 3, 2009 at 3:40 PM, Ryan Neve <ryan.neve@...> wrote:

I tried all sorts of things, but finally, by setting aspect=False I got it to work. In the documentation, the table says this defaults to True and the explanation of aspect below says it defaults to False. Although I don't entirely understand what is going on, I think this threw me off.
So then I had this:

Can you be more specific about which documentation says the default aspect is False? This may need to be fixed. Note that AxesGrid is designed for displaying images with aspect=True. Otherwise, you may better stick to the subplot..

... which looks much better, except that there are two sets of x and y axis labels? This seems to have something to do with the colorbar. I've got:

To me, there is another axes underneath the AxesGrid. It is hard to tell without a complete code.

                    label_mode = "L",
                    cbar_location="right",
                    cbar_mode="each",

                    cbar_size="2%",
                    cbar_pad="0.5%"

Now I'm trying to get scales and labels on my colorbars.
I tried:
for i,parameter in enumerate(z_dim):
    ax = my_grid[i].pcolor(x_grid,y_grid,z_dim[parameter]) # This is the pcolor plot
    my_grid[i].set_ylabel('Depth') # Correctly puts a y label on every plot.
    cb = my_grid.cbar_axes[i].colorbar(ax) # Puts in a colorbar for this axes?s
    cb.set_ylabel(parameter) #It would be nice if this was on the far right next to the colorbar. I don't see it anywhere. Perhaps underneath something?

The label of the colorbar is set to invisible by default (this is a bug). So, try something like

my_grid.cbar_axes[i].set_ylabel(parameter)

my_grid.cbar_axes[i].axis["right"].toggle(ticklabels=True,

label=True)

It looks like perhaps the colorbar axes is inside the ax axes rather than besides it?
In the demo_grid_with_each_cbar example, how would you put a scale and label on the colorbar like in this plot:?

I can put a y_label on each contour plot, but since they all have depth, I'd like to label this only once.
Is there a way to label the entire AxesGrid (or is that subplot?)?

Does label_mode="1" do what you want?

You may manually make some of the labels invisible.

Please post a "complete", but simple, script that reproduces your problem. Otherwise, it is hard to track down what is wrong.

Also, please report what version of matplotlib you're using. The axes_grid toolkit is relatively new and some of the feature may not work in older versions.

Regards,

-JJ

Thank you very much for your help,

-Ryan

On Wed, Dec 2, 2009 at 10:21 PM, Jae-Joon Lee <lee.j.joon@...> wrote:

This happens because, when the AxesGrid is created, gca() is set to the last axes, which is the last colobar axes.

If you use axes_grid toolkit, you'd better not use pyplot command that works on axes. Instead, use axes method directly.

For example, instead of "pyplot.pcolor(..)" , use "ax.pcolor(..)".

Regards,

-JJ

On Wed, Dec 2, 2009 at 2:18 PM, Ryan Neve <ryan.neve@...> wrote:

Hello,

I'm trying to use AxesGrid but I'm running into a problem:
I can plot a single pcolor plot:

But when I try to use AxesGrid, my pcolor plot is ending up where I expect my colorbar to be.

I want to have up to 6 of these plots stacked vertically, sharing a common time axis and y (depth) scale.

I'll try to simplify my code to show what I'm doing:

# I have arrays x_grid and y_grid for time and water depth.
# z_dim is a dictionary of arrays (one for each plot)
# In the plot above it has two arrays.
from matplotlib import pyplot
nrows = len(z_dim) # Number of rows is the number of arrays
My_figure = pyplot.figure(1,(8,8))
my_grid = AxesGrid(My_figure, 111, #Is this always 111?
                nrows_ncols = (nrows,1), # Always one column
                axes_pad = 0.1,
                add_all=True,
                share_all=True, # They all share the same time and depth scales
                label_mode = "L",
                cbar_location="right",
                cbar_mode="each",
                cbar_size="7%",
                cbar_pad="2%",
                )
for row_no,parameter in enumerate(z_dim):
    ax = my_grid[row_no]
    ax = pyplot.pcolor(x_grid,y_grid,z_dim[parameter])
pyplot.draw()
pyplot.show()

I eventually want to end up with something like this matlab output (which I didn't generate):

but without the duplication of x scales.

I'm new to pyplot and even after reading the documentation much of this is baffling.

-Ryan

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Re: Plotting curves filled with nonuniform color patch

2009-12-03T12:58:56Z

line 1486 of _backend_agg.cpp says

/* TODO: Support clip paths */

So, it seems that, apparently, clipping with arbitrary path has not
been implemented yet for gouraud shading (pcolormesh will be properly
clipped if shading is not used).
I hope Michael pick this up some time soon.

Meanwhile, you may open a feature request ticket on this.

Regards,

-JJ

On Wed, Dec 2, 2009 at 5:13 PM, Tony S Yu <tsyu80@...> wrote:

>
> On Dec 2, 2009, at 3:53 PM, Tony S Yu wrote:
>
>> Hi,
>>
>> I'm having hard time understanding some of the differences between functions used to plot color patches (not sure what to call them).
>>
>> I'm trying to fill a curve with a nonuniform color patch (like fill or fill_between but the color in the patch varies). I've attached code that almost does what I want; my question concerns the color patch (which is created by the call to plt.pcolor in the code below). I'd like to have nonuniform grid spacing in the color values, and also shading (i.e. interpolation of color between points). Here's what I understand:
>>
>> pcolor: allows nonuniform grid spacing, but it doesn't do shading.
>>
>> imshow: allows color shading, but requires uniform spacing
>>
>> pcolormesh: allows color interpolation and nonuniform grid spacing
>>
>> pcolormesh seems like the ideal candidate, but when I replace pcolor with pcolormesh (code commented out below pcolor call), the path doesn't get clipped by set_clip_path (but no errors are raised); in other words, the color shading fills the entire plot area. Is this a bug?
>>
>> Is there a way of making this plot work that I've overlooked?
>>
>> Thanks!
>> -Tony
>
>
> Nevermind, I found NonUniformImage after some digging. The working code is attached below if anyone is interested.
>
> If anyone knows the answer, I'm still curious if the clipping behavior for pcolormesh is a bug.
>
> Thanks,
> -Tony
>
>
>
> #~~~~ example code
>
> import numpy as np
> import matplotlib.pyplot as plt
> from matplotlib.image import NonUniformImage
>
>
> def nonuniform_imshow(x, y, C, **kwargs):
> """Plot image with nonuniform pixel spacing.
>
> This function is a convenience method for calling image.NonUniformImage.
> """
> ax = plt.gca()
> im = NonUniformImage(ax, **kwargs)
> im.set_data(x, y, C)
> ax.images.append(im)
> return im
>
>
> def plot_filled_curve(x, y, c):
> """Plot curve filled with linear color gradient
>
> Parameters
> ----------
> x, y : arrays
> points describing curve
> c : array
> color values underneath curve. Must match the lengths of `x` and `y`.
> """
> # add end points so that fill extends to the x-axis
> x_closed = np.concatenate([x[:1], x, x[-1:]])
> y_closed = np.concatenate([[0], y, [0]])
> # fill between doesn't work here b/c it returns a PolyCollection, plus it
> # adds the lower half of the plot by adding a Rect with a border
> patch, = plt.fill(x_closed, y_closed, facecolor='none')
> im = nonuniform_imshow(x, [0, y.max()], np.vstack((c, c)),
> interpolation='bilinear', cmap=plt.cm.gray)
> im.set_clip_path(patch)
>
> if __name__ == '__main__':
> line = np.linspace(0, 1, 6)
> x = np.hstack((line, [1, 2]))
> y = np.hstack((line**2, [1, 1]))
> c = np.hstack((line, [0, 0]))
> plot_filled_curve(x, y, c)
> plt.show()
>
>
>
> ------------------------------------------------------------------------------
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> a free event focused on virtualization and cloud computing.
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>

Re: AxesGrid problem.

2009-12-03T12:40:08Z

Thank You,
I think I have a better understanding. In my figure, there are six axes, three for the plots: grid[i] and three for their colorbars: grid.cbar_axes[i].
I changed my code as you suggested and got something like:

I tried all sorts of things, but finally, by setting aspect=False I got it to work. In the documentation, the table says this defaults to True and the explanation of aspect below says it defaults to False. Although I don't entirely understand what is going on, I think this threw me off.
So then I had this:

... which looks much better, except that there are two sets of x and y axis labels? This seems to have something to do with the colorbar. I've got:
                    label_mode = "L",
                    cbar_location="right",
                    cbar_mode="each",
                    cbar_size="2%",
                    cbar_pad="0.5%"

Now I'm trying to get scales and labels on my colorbars.
I tried:
for i,parameter in enumerate(z_dim):
    ax = my_grid[i].pcolor(x_grid,y_grid,z_dim[parameter]) # This is the pcolor plot
    my_grid[i].set_ylabel('Depth') # Correctly puts a y label on every plot.
    cb = my_grid.cbar_axes[i].colorbar(ax) # Puts in a colorbar for this axes?s
    cb.set_ylabel(parameter) #It would be nice if this was on the far right next to the colorbar. I don't see it anywhere. Perhaps underneath something?

It looks like perhaps the colorbar axes is inside the ax axes rather than besides it?
In the demo_grid_with_each_cbar example, how would you put a scale and label on the colorbar like in this plot:?

I can put a y_label on each contour plot, but since they all have depth, I'd like to label this only once.
Is there a way to label the entire AxesGrid (or is that subplot?)?

Thank you very much for your help,

-Ryan

On Wed, Dec 2, 2009 at 10:21 PM, Jae-Joon Lee <lee.j.joon@...> wrote:

This happens because, when the AxesGrid is created, gca() is set to the last axes, which is the last colobar axes.

If you use axes_grid toolkit, you'd better not use pyplot command that works on axes. Instead, use axes method directly.

For example, instead of "pyplot.pcolor(..)" , use "ax.pcolor(..)".

Regards,

-JJ

On Wed, Dec 2, 2009 at 2:18 PM, Ryan Neve <ryan.neve@...> wrote:

Hello,

I'm trying to use AxesGrid but I'm running into a problem:
I can plot a single pcolor plot:

But when I try to use AxesGrid, my pcolor plot is ending up where I expect my colorbar to be.

I want to have up to 6 of these plots stacked vertically, sharing a common time axis and y (depth) scale.

I'll try to simplify my code to show what I'm doing:

# I have arrays x_grid and y_grid for time and water depth.
# z_dim is a dictionary of arrays (one for each plot)
# In the plot above it has two arrays.
from matplotlib import pyplot
nrows = len(z_dim) # Number of rows is the number of arrays
My_figure = pyplot.figure(1,(8,8))
my_grid = AxesGrid(My_figure, 111, #Is this always 111?
                nrows_ncols = (nrows,1), # Always one column
                axes_pad = 0.1,
                add_all=True,
                share_all=True, # They all share the same time and depth scales
                label_mode = "L",
                cbar_location="right",
                cbar_mode="each",
                cbar_size="7%",
                cbar_pad="2%",
                )
for row_no,parameter in enumerate(z_dim):
    ax = my_grid[row_no]
    ax = pyplot.pcolor(x_grid,y_grid,z_dim[parameter])
pyplot.draw()
pyplot.show()

I eventually want to end up with something like this matlab output (which I didn't generate):

but without the duplication of x scales.

I'm new to pyplot and even after reading the documentation much of this is baffling.

-Ryan

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numpy loadtxt and comments

2009-12-03T11:15:01Z

Hi All

Not really about matplotlib, but since the load() function was removed
it seems we have to use numpy.loadtxt in stead.
I'm reading some datafiles that have comment line beginning with both
'#' and '@'. Is there a way to assign two different values to the
'comments' keyword?

Thanks, Peter

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Re: How to display axis numbers inside the figure area

2009-12-03T10:37:43Z

Hi Angelica,

I have to admit I don't get the point of what you want to do and maybe this is
true for others too. I tried something (see attachement), but maybe it is
better if you could set up an small example script or draw a picture of what
you want to see finally.

Kind regards,
Matthias

On Monday 30 November 2009 18:09:29 Pekeika wrote:

> Good morning All,
>
> I am creating figures that need to overlay with maps, so disabling the box
> around my figures is a must. (need no title, legend, etc...) I have my
> plain figure now without surroundings but now need the axis numbers "on"
> the grid inside the plot area (like latitude and longitude numbers appear
> next to the grids on maps)... I cannot find a function or an argument for
> the axis() or axes() functions that translates axes into the plot area...
> Any ideas please?
>
> Thank you so much,
> Angelica.

axes_numbers.png (10K) Download Attachment
axes_numbers.py (259 bytes) Download Attachment

Re: Cross axis arrows

2009-12-03T10:30:04Z

You need to add the patch to the second axes.

patch = ConnectionPatch((.5, .5), (.7, .3), 'data', 'data',
axesA=ax1, axesB=ax2,
zorder=100, arrowstyle='fancy',
connectionstyle='Angle3',
mutation_scale=10)
ax2.add_patch(patch)

However, this does not work right out of the box currently (which
should be bug).
As a workaround, add a following line and it will work.

patch.set_annotation_clip(False)

It would be appreciated if you file a bug report for a future reference.

http://sourceforge.net/tracker/?atid=560720&group_id=80706&func=browse

Regards,

-JJ

On Thu, Dec 3, 2009 at 9:31 AM, Stephane Raynaud
<stephane.raynaud@...> wrote:

> Hi,
>
> how to make this arrow not disappear below the right plot?
> Here is the code :
>
> ------------------------------------------------------------
> from matplotlib.patches import *
> import matplotlib.pyplot as P
>
> P.figure(figsize=(5, 3))
> ax1 = P.subplot(121)
> P.plot([0, 1])
> ax2 = P.subplot(122)
> P.plot([0, 1])
>
>
> patch = ConnectionPatch((.5, .5), (.7, .3), 'data', 'data', axesA=ax1,
> axesB=ax2,
> zorder=100, arrowstyle='fancy',clip_on=False, connectionstyle='Angle3',
> mutation_scale=100)
> ax1.add_patch(patch)
>
> P.savefig('cross_arrow.png')
> P.show()
> ------------------------------------------------------------
>
>
>
>
> --
> Stephane Raynaud
>
> ------------------------------------------------------------------------------
> Join us December 9, 2009 for the Red Hat Virtual Experience,
> a free event focused on virtualization and cloud computing.
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>
>

Re: usetex=True and savefig(eps-file)

2009-12-03T10:26:01Z

Hi Jouni,

thanks again for your advice.

I don't think that I do have 'some setting that causes temporary files to end
up in the root directory", because my system is more or less kubuntu (8.04)
out of the box.

But maybe you are nevertheless right, because in tmp there are ./root
and ./lost+found, which I am not allowed to enter.
Finally this error is due to the behaviour of ps-backend and my TEX-path,
which searches in all sub-directories.

Thanks a lot for your time and advice to locate the root of the strange
behaviour.

Kind regards,
Matthias

On Thursday 03 December 2009 19:04:55 Jouni K. Seppänen wrote:

> Matthias Michler <MatthiasMichler@...> writes:
> > Do you know why is happens only for ps/eps-files?
>
> The ps backend uses TeX in a different way than the other backends. It
> uses psfrag and dvips to construct the final file.
>
> >> Have you set any TeX-related environment variables or edited any
> >> configuration files? What does "kpsepath tex" print?
> >
> > in my .zshrc I set
> > TEXINPUTS=~/Texte/Styles//:.//:
>
> It's probably the .// entry, which causes TeX to search all
> subdirectories of the current directory. The ps backend does something
> like
>
> cd /tmp && latex file.tex
>
> so it should just look in subdirectories of the temporary directory, but
> perhaps it somehow goes awry. Do you have some setting that causes
> temporary files to end up in the root directory?

Re: usetex=True and savefig(eps-file)

2009-12-03T10:04:55Z

Matthias Michler <MatthiasMichler@...> writes:

> Do you know why is happens only for ps/eps-files?

The ps backend uses TeX in a different way than the other backends. It
uses psfrag and dvips to construct the final file.

>> Have you set any TeX-related environment variables or edited any
>> configuration files? What does "kpsepath tex" print?
>
> in my .zshrc I set
> TEXINPUTS=~/Texte/Styles//:.//:

It's probably the .// entry, which causes TeX to search all
subdirectories of the current directory. The ps backend does something
like

cd /tmp && latex file.tex

so it should just look in subdirectories of the temporary directory, but
perhaps it somehow goes awry. Do you have some setting that causes
temporary files to end up in the root directory?

--
Jouni K. Seppänen
http://www.iki.fi/jks

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Cross axis arrows

2009-12-03T06:31:55Z

Hi,

how to make this arrow not disappear below the right plot?
Here is the code :

------------------------------------------------------------
from matplotlib.patches import *
import matplotlib.pyplot as P

P.figure(figsize=(5, 3))
ax1 = P.subplot(121)
P.plot([0, 1])
ax2 = P.subplot(122)
P.plot([0, 1])

patch = ConnectionPatch((.5, .5), (.7, .3), 'data', 'data', axesA=ax1, axesB=ax2,
zorder=100, arrowstyle='fancy',clip_on=False, connectionstyle='Angle3', mutation_scale=100)
ax1.add_patch(patch)

P.savefig('cross_arrow.png')
P.show()
------------------------------------------------------------

--
Stephane Raynaud

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cross_arrow.png (20K) Download Attachment

Re: Extending patches.Rectangle class

2009-12-03T01:16:54Z

Jae-Joon Lee <lee.j.joon@...> writes:
<...>

>
> It depends on your mileage.
>
> However, a patch in matplotlib usually means a closed path. If you add
> additional lines, you need to be careful not to mess the filling of
> the rectangle.
>
> I guess it would better to simply use separate artists for additional
> lines you want. You may create a container artist for patches and
> lines if you want.
>
> Regards,
>
> -JJ

Thanks, that's sounds like a better way indeed. I'll work in this direction.

Jorge

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Re: usetex=True and savefig(eps-file)

2009-12-03T01:12:50Z

Hi Jouni,

Thanks for your explaination.

On Wednesday 02 December 2009 17:20:37 Jouni K. Seppänen wrote:

> Matthias Michler <MatthiasMichler@...> writes:
> > ./root/article.cls.tex: Permission denied
> > ./root/article.cls: Permission denied
> > ./lost+found/article.cls.tex: Permission denied
> > ./lost+found/article.cls: Permission denied
> > ./root/article.cls.tex: Permission denied
> > ./root/article.cls: Permission denied
> > ./lost+found/article.cls.tex: Permission denied
> > ./lost+found/article.cls: Permission denied
>
> That looks like a TeX configuration problem. I'm guessing that when TeX
> encounters \documentclass{article}, it asks the path-searching library
> for "article.cls", and for some reason /root and /lost+found are
> included in the path. You don't have permission as normal user to access
> these directories, so the library causes error messages to be printed.
> The path probably also includes the correct directories, so the search
> eventually succeeds, but then article.cls wants to input size10.clo,
>
> causing a new round of errors:
> > ./root/size10.clo.tex: Permission denied
> > ./root/size10.clo: Permission denied
>
> (etc)

Do you know why is happens only for ps/eps-files?

> Have you set any TeX-related environment variables or edited any
> configuration files? What does "kpsepath tex" print?

in my .zshrc I set
TEXINPUTS=~/Texte/Styles//:.//:
export TEXINPUTS

and "$ kpsepath tex" yields
/home/michler/Texte/Styles//:.//:.:/home/michler/.texmf-config/tex/kpsewhich//:/home/michler/.texmf-var/tex/kpsewhich//:/home/michler/texmf/tex/kpsewhich//:/etc/texmf/tex/kpsewhich//:!!/var/lib/texmf/tex/kpsewhich//:!!/usr/local/share/texmf/tex/kpsewhich//:!!/usr/share/texmf/tex/kpsewhich//:!!/usr/share/texmf-texlive/tex/kpsewhich//:/home/michler/.texmf-config/tex/generic//:/home/michler/.texmf-var/tex/generic//:/home/michler/texmf/tex/generic//:/etc/texmf/tex/generic//:!!/var/lib/texmf/tex/generic//:!!/usr/local/share/texmf/tex/generic//:!!/usr/share/texmf/tex/generic//:!!/usr/share/texmf-texlive/tex/generic//:/home/michler/.texmf-config/tex///:/home/michler/.texmf-var/tex///:/home/michler/texmf/tex///:/etc/texmf/tex///:!!/var/lib/texmf/tex///:!!/usr/local/share/texmf/tex///:!!/usr/share/texmf/tex///:!!/usr/share/texmf-texlive/tex///

Furthermore I did (as root):
$ cd /root $ cd /lost+found/ and $ cd /tmp/
and
$ ls **/*tex **/*.cls
but always got
ls: cannot access **/*tex: No such file or directory
ls: cannot access **/*.cls: No such file or directory
... That means there are no tex or cls-files.

Do you have any idea what's wrong?

Kind regards,
Matthias

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Re: mplot3d: plot_surface() and contour on grid?

2009-12-03T01:01:15Z

Thanks a lot!

Regards,
Matthias

On Wednesday 02 December 2009 17:10:54 Reinier Heeres wrote:

> Hi Matthias,
>
> I have a similar patch lying around somewhere, and I will try to apply
> it soon. I've been terribly busy lately, but I expect some nice
> mplot3d enhancements in the very near future.
>
> Regards,
> Reinier
>
> On Wed, Dec 2, 2009 at 4:22 PM, Matthias Michler
>
> <MatthiasMichler@...> wrote:
> > Hi Andrew,
> >
> > do you have any idea if the patch (or a part of it) may get a part of
> > matplotlib-svn some day?
> >
> > Kind regards,
> > Matthias
> >
> > On Friday 09 October 2009 23:25:28 Andrew Straw wrote:
> >> Matthias Michler wrote:
> >> > Hello list,
> >> >
> >> > I'm not an expert in axes3d, but in case the feature which Nicolas
> >> > requested is not possible in an easy manner up to now, I propose an
> >> > additional kwarg for axes3d.Axes3D.contour. Something like *offset*.
> >> > If offset is None the z-values of the contour lines corresponds to
> >> > given Z and otherwise offset is used for the z-values of the contour
> >> > lines. I attached a changed axes3d.py and a patch against current svn.
> >> > The result is illustrated in the contour3d_demo.png.
> >> >
> >> > Could any of the experts have a look at it and tell me if this could
> >> > be useful, please?
> >> >
> >> > Thanks in advance for any comments.
> >> >
> >> > Kind regards
> >> > Matthias
> >> >
> >> > On Wednesday 30 September 2009 19:22:42 Nicolas Bigaouette wrote:
> >> >> Hi,
> >> >> I have a nice plot_surface() using mplot3d (see attachement).
> >> >>
> >> >> I'd like to project the surface on the axis xoy, xoz and yoz with a
> >> >> contour, similar to this figure:
> >> >> http://homepages.ulb.ac.be/~dgonze/INFO/matlab/fig19.jpg
> >> >>
> >> >> Is it possible using matplotlib and mplot3d?
> >> >>
> >> >> Thanx!
> >>
> >> Hi Matthias,
> >>
> >> I committed your patch to a github branch of MPL, but I'll let Reinier
> >> actually commit something based on this to MPL.
> >> http://github.com/astraw/matplotlib/tree/dev/michler-3d-contourf-offsets
> >>
> >> -Andrew

Re: Output to any vector format openoffice can use

2009-12-03T00:48:55Z

Thak you very much for pointing this out to me. I was not aware that Inkscape is able to output to .odg. Unfortunatly export into .odg works badly. I converted .svg files, and both were rendered totally incorrect. All the axes labels vanished, in a lineplot it connected the end of the line to the origin, leading to a diagonal line which should not be there, and the rasterized image included by pcolorfast was also not included. Therefore I fear that exporting into .odg is not a usable alternative.

Re: countour plot custom labels

2009-12-02T20:36:13Z

This would only meaningful if you set contour levels manually.

plt.figure()
levels = [-1, 0, 1]
fmt = {-1.:"-1",
0.:"0",
1.:"+1"}
CS = plt.contour(X, Y, Z, levels)
plt.clabel(CS, inline=1, fontsize=10, fmt=fmt)

Regards,

-JJ

On Wed, Dec 2, 2009 at 6:32 AM, Momme Butenschön <mommebu@...> wrote:

> in the help for the countour plot labeling it says:
>       *fmt*:
>         a format string for the label. Default is '%1.3f'
>         Alternatively, this can be a dictionary matching contour
>         levels with arbitrary strings to use for each contour level
>         (i.e., fmt[level]=string)
> can somebody enlighten me how this works?
> how do I connect levels to what dictionary keyword?
>
> thank a lot,
> Momme
>
>
> ------------------------------------------------------------------------------
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Re: Extending patches.Rectangle class

2009-12-02T19:34:35Z

On Tue, Dec 1, 2009 at 8:48 AM, Jorge Scandaliaris
<jorgesmbox-ml@...> wrote:
> How difficult would be to extend the Rectangle class so besides its permimeter
> it draws lines showing halfs or thirds of the width and height?

It depends on your mileage.

However, a patch in matplotlib usually means a closed path. If you add
additional lines, you need to be careful not to mess the filling of
the rectangle.

I guess it would better to simply use separate artists for additional
lines you want. You may create a container artist for patches and
lines if you want.

Regards,

-JJ

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Re: AxesGrid problem.

2009-12-02T19:21:43Z

This happens because, when the AxesGrid is created, gca() is set to the last axes, which is the last colobar axes.

If you use axes_grid toolkit, you'd better not use pyplot command that works on axes. Instead, use axes method directly.

For example, instead of "pyplot.pcolor(..)" , use "ax.pcolor(..)".

Regards,

-JJ

On Wed, Dec 2, 2009 at 2:18 PM, Ryan Neve <ryan.neve@...> wrote:

Hello,

I'm trying to use AxesGrid but I'm running into a problem:
I can plot a single pcolor plot:

But when I try to use AxesGrid, my pcolor plot is ending up where I expect my colorbar to be.

I want to have up to 6 of these plots stacked vertically, sharing a common time axis and y (depth) scale.

I'll try to simplify my code to show what I'm doing:

# I have arrays x_grid and y_grid for time and water depth.
# z_dim is a dictionary of arrays (one for each plot)
# In the plot above it has two arrays.
from matplotlib import pyplot
nrows = len(z_dim) # Number of rows is the number of arrays
My_figure = pyplot.figure(1,(8,8))
my_grid = AxesGrid(My_figure, 111, #Is this always 111?
                nrows_ncols = (nrows,1), # Always one column
                axes_pad = 0.1,
                add_all=True,
                share_all=True, # They all share the same time and depth scales
                label_mode = "L",
                cbar_location="right",
                cbar_mode="each",
                cbar_size="7%",
                cbar_pad="2%",
                )
for row_no,parameter in enumerate(z_dim):
    ax = my_grid[row_no]
    ax = pyplot.pcolor(x_grid,y_grid,z_dim[parameter])
pyplot.draw()
pyplot.show()

I eventually want to end up with something like this matlab output (which I didn't generate):

but without the duplication of x scales.

I'm new to pyplot and even after reading the documentation much of this is baffling.

-Ryan

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Re: Output to any vector format openoffice can use

2009-12-02T18:17:21Z

Inkscape's native format is svg and it exports in .odg, which OO should be able to use. I did a test combining a svg vector and png raster and then saving as .odg, and it wrote the file. But I don't have OO so I can't try to import the result.

regards,
Gary B

marcusantonius wrote:

I am searching a way, so that I can insert my matplotlib graphs as vector data in openoffice. I make colormaps using pcolorfast. If I save the figure as emf, the colormap inside the axes vanishes, because the normal emf backend cannot include rasterized data. Is there any way (e.g. using a different backend) which gives emf/wmf files which contain the rasterized data?

Is there a convertor from svg to emf which can do the trick? (I tried uniconvertor but it also looses the rasterized data). I tried to insert svg/eps/pdf files into openoffice, but the results are less than promising