matplotlib-users — Discussion related to using matplotlib

[Matplotlib-users] 3d surfaces in basemap?

[Andreas H. <li...@hi...>]

Hi, maybe matplotlib is capable of doing this:

I have two gridded datasets, A and B, for say Europe. Now I want to plot
a 3d surface with the z-values given by dataset A. The surface should be
colored using a given color palette and the values from dataset B.

Any ideas on how to do this are greatly appreciated =)

Cheers, Andreas.

[Matplotlib-users] rasterized colorbar

[Jody K. <jk...@uv...>]

Hi all,

So I figured out the magic of "rasterized=True", which is *really* helpful!

However, the colorbar doesn't seem to accept rasterized=True, so there are little lines every facet (zoom on the attached pdf).  Is there another way to get the colorbar colors rasterized?

Thanks Jody

x = linspace(0,1,1000)
X = outer(x,x)
pcolormesh(X,cmap=get_cmap('RdBu_r',lut=32),rasterized=True)
colorbar()
savefig('Test.pdf',dpi=50)

Re: [Matplotlib-users] how to express statistical data in colors

[Chloe L. <ch...@be...>]

Chloe Lewis 
PhD candidate, Harte Lab
Division of Ecosystem Sciences, ESPM
University of California, Berkeley
137 Mulford Hall
Berkeley, CA  94720
ch...@be...

Begin forwarded message:

> From: Chloe Lewis <ch...@be...>
> Subject: Re: [Matplotlib-users] how to express statistical data in colors
> Date: October 26, 2012 10:47:54 AM PDT
> To: ra...@0x...
> 
> you'll be doing something like the second color bar, but making the boundary and color definitions a lot more flexible. Where the discrete color bar uses
> 
> cmap = mpl.colors.ListedColormap(['r', 'g', 'b', 'c'])
> bounds = [1, 2, 4, 7, 8]
> you'll be making a whole LinearSegmentedColormap, see
> http://matplotlib.org/api/colors_api.html#matplotlib.colors.LinearSegmentedColormap
> and check out specifically the ascii-art explanation of interpolation between row[i] and row[i+1]. Red, green, blue will break based on your data density and how you want to express 'intensity'. And depending on whether you'll make it red-green-colorblindness neutral!
> Interesting problem. Has it been implemented in some other software?
> 
> Chloe Lewis 
> PhD candidate, Harte Lab
> Division of Ecosystem Sciences, ESPM
> University of California, Berkeley
> 137 Mulford Hall
> Berkeley, CA  94720
> ch...@be...
> 

[Matplotlib-users] how to express statistical data in colors

[<ra...@0x...>]

hi,

I'd like to present data in a colorbar-style graphic.

The data to plot is in this form: [1,2,4,4,4.1,4.3,6,7].
The colorbar with this data should show at the begin the color with low
intensity. In more or less the middle of the colorbar the intensity
should be much more because there are a lot values around 4-4.3 and at
the end the intensity should be low again. I imagine low to middle
intensity to show with the color blue and high intensity with nearly by
or with the color black.

With colobar-style I mean this:
http://matplotlib.org/examples/api/colorbar_only.html (the first bar).

I assume matplotlib already provides such a method I cant find.. so any
input is welcome:)

thank you

Re: [Matplotlib-users] Would like to update visible plot using pyside and matplotlib

[troyrock <tro...@ro...>]

I figured out the problem.  I need to call self.canvas.draw() in order to
update the image.  Sorry for the email.



--
View this message in context: http://matplotlib.1069221.n5.nabble.com/Would-like-to-update-visible-plot-using-pyside-and-matplotlib-tp39576p39577.html
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[Matplotlib-users] Would like to update visible plot using pyside and matplotlib

[troyrock <tro...@ro...>]

I have a tool to show information extracted from various experiments and then
stored in a database.  I would like to update a plot shown in the lower half
of the window when information such as the ranges of variables are modified
in the upper half.  I can initially put data into the plot, however when I
want to change the contents (such as add another line to the plot), the 
changes don't get displayed.  Here is some code to illustrate the problem:

import matplotlib
matplotlib.rcParams['backend.qt4'] = 'PySide'
import matplotlib.pyplot as plt
from matplotlib.figure import Figure
matplotlib.use('Qt4Agg')
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as
FigureCanvas
from PySide import QtCore, QtGui
import sys


class TabDialog(QtGui.QDialog):
   def __init__(self):
      super(TabDialog, self).__init__()

      tabWidget = QtGui.QTabWidget()
      tabWidget.addTab(AnalyzeTab(), self.tr("Analyze"))

      buttonLayout = QtGui.QHBoxLayout()
      saveButton = QtGui.QPushButton(self.tr("Update"))
      saveButton.clicked[bool].connect(self.update)
      buttonLayout.addWidget(saveButton)

      mainLayout = QtGui.QVBoxLayout()
      mainLayout.addWidget(tabWidget)
      mainLayout.addLayout(buttonLayout)
      self.setLayout(mainLayout)

   def update(self):
      data.update()

class DataHolder():
   def __init__(self):
      self.gFig = Figure()
      self.ax = self.gFig.add_subplot(111)
      self.ax.plot([1,2,4,0.1])
      self.canvas = FigureCanvas(self.gFig)

   def update(self):
      self.ax.plot([8,6,4,2])

class AnalyzeTab(QtGui.QWidget):
   def __init__(self, parent=None):
      QtGui.QWidget.__init__(self, parent)

      analyzeLayout = QtGui.QGridLayout()
      analyzeLayout.addWidget(data.canvas, 2, 0, 6, 8)

      self.setLayout(analyzeLayout)

if __name__ == "__main__":
   app = QtGui.QApplication(sys.argv)

   data = DataHolder()

   tabdialog = TabDialog()
   tabdialog.show()
   sys.exit(app.exec_())

Any suggestions are very much appreciated.



--
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Re: [Matplotlib-users] Histogram with overlapping bins

[fiolj <fi...@ya...>]

Hi, some time ago I needed the same thing and hacked the function
histogram (from numpy or matplo. Here goes my function

## Calculates the histogram allowing for overlapping bins, which are
given by
#
# @param a
# @param bins a sequence of pairs (left,right), limits for each bin
#
# @return hist (numpy array)
#         bin_centers (numpy array)
def myhistogram(a, bins):
  """
  Compute the histogram of a set of data.

  Parameters
  ----------
  a : array_like
      Input data.
  bins : sequence of pairs
      It defines the bin edges (left,right), allowing for non-uniform
bin widths.

  Returns
  -------
  hist : array
    The values of the histogram. See `normed` and `weights` for a
    description of the possible semantics.
  bin_centers : array of dtype float
    Return the bin centers ``(length(hist))``.

  Notes
  -----
  All but the last (righthand-most) bin is half-open.  In other words, if
  `bins` is::

    [1, 2, 3, 4]

  then the first bin is ``[1, 2)`` (including 1, but excluding 2) and the
  second ``[2, 3)``.  The last bin, however, is ``[3, 4]``, which *includes*
  4.

  Examples
  --------
  >>> myhistogram([1,2,1], bins=[(0,1),(1,1.5),(1.5,2.5),(2,3)])
  (array([0.5, 1.25, 2, 2.5]), array([0, 0, 1, 2, 3]))
  """
  bins = np.asarray(bins)               # bins are 2-dimensional arrays
of shape (n,2)
  if len(bins.shape) != 2 or bins.shape[1] != 2:
    raise AttributeError, 'bins must be a list/array of 2-tuples.'

  a = np.asarray(a)
  a =  a.ravel()
  n = np.zeros(len(bins), int)

  block = 65536
  for i in np.arange(0, len(a), block):
    sa = np.sort(a[i:i+block])
    n += np.r_[sa.searchsorted(bins[:-1,1], 'left'),
sa.searchsorted(bins[-1,1], 'right')]\
         - np.r_[sa.searchsorted(bins[:-1,0], 'left'),
sa.searchsorted(bins[-1,0], 'right')]
  return n, (bins[:,0]+bins[:,1])/2.

[Matplotlib-users] time taken to savefig

[Larry C. <lar...@gm...>]

Hi

I have been doing some work that generates a lot of plots and since the
plots were taking a long time I looked into to whether I could speed up the
process.

I found some information on how I might improve things from the following
link:
http://stackoverflow.com/questions/11688318/how-to-speed-up-matplotlib-when-plotting-and-saving-lots-of-figureswhich
showa that you can speed things up by using the same axes and simply
updating the line data.

When I adapted this idea to my plots I noticed that, though the plot loop
was quicker my script was running slower. I wrote a code snippet to repeat
the problem - shown below:
#!/usr/bin/env python
import os, matplotlib, time
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
import numpy as np
from cmpactionresultsbetweenviews_1 import getPlotHtml

allActionPlotLists = [[0,  1,  2 ,  3, 4,  5,  6,  7, 8,  9],
                      [ 10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
                      [9,8,7,6,5,4,3,2,1,0],
                      [19,18,17,16,15,14,13,12,11,10]]
allActionLegendsLists = [str(i) for i in range(len(allActionPlotLists[0]))]

legendProps={'labelspacing':0.5, 'prop':{'size':8}}
colours=['b+-', 'r+-', 'g+-', 'k+-', 'c+-', 'm+-', 'bD:', 'rD:', 'gD:',
'kD:']
fig = plt.figure()
ax = None
plotlines = [None for i in range(len(allActionPlotLists))]
savedir = "tmpRes"
if not os.path.exists(savedir):
    os.makedirs(savedir)
figSrcFnRoot = "plotFil"
fil = open(os.path.join(savedir, "savepng.html"), 'w')

xlabel = "x label"
ylabel = "values"
colours=['b+-', 'r+-', 'g+-', 'k+-', 'c+-', 'm+-', 'bD:', 'rD:', 'gD:',
'kD:']

for i in range(20):
    start_plot_time = time.time()
    plottitle = "Plot %d" % (i)
    fig.suptitle("")
    fig.suptitle(plottitle)

    for subPltIdx in range(len(allActionPlotLists)):
        li = allActionPlotLists[subPltIdx]
        if ax == None:
            ax = fig.add_subplot(1,1,1)
            ax.set_xlabel(xlabel)
            ax.set_ylabel(ylabel)

        if plotlines[subPltIdx] == None:
            ax.set_xlabel(xlabel)
            ax.set_ylabel(ylabel)
            plotlines[subPltIdx] = ax.plot(range(len(li)), li,
colours[subPltIdx])[0]
        else:
            plotlines[subPltIdx].set_ydata(li)
            plotlines[subPltIdx].set_xdata(range(len(li)))

    fig.legend(plotlines, allActionLegendsLists, labelspacing=0.5,
prop=legendProps['prop'])
    # **** change the above line for the one below and the increasing save
time problem goes away
    #ax.legend(plotlines, allActionLegendsLists, labelspacing=0.5,
prop=legendProps['prop'])
    print "plot Execution time:", time.time()-start_plot_time

    figfn = "%s_%d" % (figSrcFnRoot, i)
    figfnlink = figfn.replace('%',
'%25').replace(';','%3b').replace(':','%3A')
    fn = os.path.join(savedir, "%s.png" % figfn)
    start_time = time.time()
    fig.savefig(fn, format='png',dpi=75)
    print "savefig Execution time:", time.time()-start_time
    htmlStr = ''
    htmlStr += '<center><img src="%s" alt="could not find %s
image"/></center>' % (os.path.join(".","%s.png" % figfnlink), figfn)
    fil.write(htmlStr + "<br>")
plt.close()
fil.close()

A little further investigation showed that savefig was taking longer each
run of the loop. I eventually noticed that replacing the call to
fig.legend() with ax.legend() solved the problem. Anyone know why the time
taken to save the plot increases when using fig.legend() in the code above ?

While doing this I also noticed a couple of other things:
1. I cannot seem to clear the figure title, so when I re-set it I get the
new title overlaying the old one in the plot output. Does anyone know how
to completely clear and reset the title of an existing figure ?

2. The call to figure.legend() puts the legends nicely outside the plot
boundaries (in the top right hand corner). The equivalent call to
ax.legend() places the legends inside the plot boundary. Does anyone know
a) why the behavior here is slightly different and b) how I can get the
legends outside the plot boundary using ax.legend() ?

Re: [Matplotlib-users] Histogram with overlapping bins

[fiolj <fi...@ya...>]

Hi, some time ago I needed the same thing and hacked the function
histogram (from numpy). Here goes my function, I hope it will result useful

Cheers,
	Juan

## Calculates the histogram allowing for overlapping bins, which are
given by
#
# @param a
# @param bins a sequence of pairs (left,right), limits for each bin
#
# @return hist (numpy array)
#         bin_centers (numpy array)
def myhistogram(a, bins):
  """
  Compute the histogram of a set of data.

  Parameters
  ----------
  a : array_like
      Input data.
  bins : sequence of pairs
      It defines the bin edges (left,right), allowing for non-uniform
bin widths.

  Returns
  -------
  hist : array
    The values of the histogram. See `normed` and `weights` for a
    description of the possible semantics.
  bin_centers : array of dtype float
    Return the bin centers ``(length(hist))``.

  Notes
  -----
  All but the last (righthand-most) bin is half-open.  In other words, if
  `bins` is::

    [1, 2, 3, 4]

  then the first bin is ``[1, 2)`` (including 1, but excluding 2) and the
  second ``[2, 3)``.  The last bin, however, is ``[3, 4]``, which *includes*
  4.

  Examples
  --------
  >>> myhistogram([1,2,1], bins=[(0,1),(1,1.5),(1.5,2.5),(2,3)])
  (array([0.5, 1.25, 2, 2.5]), array([0, 0, 1, 2, 3]))
  """
  bins = np.asarray(bins)               # bins are 2-dimensional arrays
of shape (n,2)
  if len(bins.shape) != 2 or bins.shape[1] != 2:
    raise AttributeError, 'bins must be a list/array of 2-tuples.'

  a = np.asarray(a)
  a =  a.ravel()
  n = np.zeros(len(bins), int)

  block = 65536
  for i in np.arange(0, len(a), block):
    sa = np.sort(a[i:i+block])
    n += np.r_[sa.searchsorted(bins[:-1,1], 'left'),
sa.searchsorted(bins[-1,1], 'right')]\
         - np.r_[sa.searchsorted(bins[:-1,0], 'left'),
sa.searchsorted(bins[-1,0], 'right')]
  return n, (bins[:,0]+bins[:,1])/2.

[Matplotlib-users] wx.aui.AuiNotebook with a matplotlib figure on each page CTRL-TAB page to page navigation does not work in OSX works in windows

[hari j. <ha...@gm...>]

Hi I am using
wxpython : 2.9.4.0
matplotlib : 1.3
osx Lion

In my application I have a number of matplotlib figure objects, one  on
each page of the wx.aui.AuiNotebook .The pages are each a figure and
arranged as tabs on the top of the wxpython frame like embedding in wx5
example from the matplotlib gallery.

On Windows I can navigate from page to page  of the Notebook using CTRL-TAB
and CTRL-SHIFT-TAB.

However on OSX -Lion  , neither the CTRL-TAB, nor Alt/Tab navigate from
page to page.

Instead what happens is that the "mouse selection" moves from icon to icon
i.e from the "Home" to the "Pan-zoom " icon on the bottom of the matplotlib
figure. The wxAuiNotebook is oblvious of these mouse events.

Does anyone know how to restore the windows os behavior where CTRL-TAB
changes the page of the Notebook on OSX. How do I prevent the matplotlib
figure object from intercepting these events.

Thanks
Hari

[Matplotlib-users] mpl_binutils: Plotting from the command-line with matplotlib

[Damon M. <dam...@gm...>]

All,

Several days ago I tested the waters and asked you guys, the
community, how useful you thought a command-line front-end to
matplotlib would be. The overwhelmingly positive feedback was enough
for me to sit down and figure out how to do this well, and in a way
that would mimic existing tools to achieve such tasks. One example
being the `graph` utility, which is a part of GNU plotutils. Though
there are subtle differences between mpl_binutils and GNU plotutils
they, in my opinion, improve the user experience and reduce the
ambiguity regarding the parsing of command-line options.

I am announcing that mpl_binutils is in a state ready to be tested by
you guys. Hopefully you'll find it useful. You can check out the
source code here: https://github.com/dmcdougall/mpl_binutils

Without getting into details, I ran into some serious limitations with
argparse. At the end of the day, nothing is perfect, but some tools
are better than others. One such tool, docopt, was shown to me by Mark
Lawrence. docopt will change the way I do any python from the
command-line in the future. docopt is a light-weight command-line
parsing library written in python with no dependencies.

mpl_binutils has two dependencies: docopt and matplotlib. Most of you
should already have one of these! For the other, a simple `pip install
docopt` should work but I had no problems installing it from source
(python setup.py install) on OS X. mpl_binutils is currently a single
script (a python script), called mpl-graph. There is example usage on
the github readme if you'd like to take a look.

Currently, mpl-graph doesn't fail gracefully. It should, but I wanted
to get something working first. Command-line option validation is next
on my todo list and since there are only a handful of command line
options implemented (albeit the most useful ones, in my opinion), this
shouldn't be too big of a job.

Go forth and fork!

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Re: [Matplotlib-users] Histogram with overlapping bins

[Damon M. <dam...@gm...>]

On Sat, Oct 20, 2012 at 11:37 PM, Benjamin Root <ben...@ou...> wrote:
>
>
> On Saturday, October 20, 2012, Damon McDougall wrote:
>>
>> On Sat, Oct 20, 2012 at 10:25 PM, Steven Boada <bo...@ph...>
>> wrote:
>> > It'd be cool if we could do something like
>> >
>> > bins = [(0.0,0.05,0.1),(0.05,0.1,0.15)...]
>> >
>> > Where I have specified the left edge, center and right edge of each
>> > bin. Yeah, that'd be pretty slick.
>> >
>> > S
>> >
>> > On Sat Oct 20 16:21:41 2012, Steven Boada wrote:
>> >> Let's say I generate a bunch of random numbers from 0-1. Then, I'd
>> >> like to make a histogram of it. But here's the clincher. I'd like my
>> >> bins to overlap a bit. For example, if the first bin is from 0 - 0.1,
>> >> centered on 0.05, I'd like the next (second) bin to be centered on 0.1
>> >> and range from 0.05 - 0.15.
>> >>
>> >> So basically, I want the width of each bin to be greater than the
>> >> spacing.
>> >>
>> >> Is this something that could be done with the histogram function? I
>> >> did a couple of google searches and couldn't come up with anything
>> >> meaningful. Apparently, 'rwidth' in the hist function just makes the
>> >> displayed bars bigger or smaller.
>> >>
>> >> Any thoughts?
>> >>
>> >
>> > --
>> >
>> > Steven Boada
>> >
>> > Doctoral Student
>> > Dept of Physics and Astronomy
>> > Texas A&M University
>> > bo...@ph...
>>
>> My thoughts are that this goes against everything a histogram is set
>> out to do; attempt to provide a 'discretised' probability distribution
>> function given a set of discrete samples. Lets say a sample lies in
>> the region where two bins overlap. How do you define which bin the
>> sample lies in? Both? If both, how do you define the value of the
>> approximated probability distribution on a bin? You could just take
>> the height of the bin, but some of the bin's mass lies in each of the
>> neighbouring bins.
>>
>> If you don't want to apply mass to the neighbouring bins for a sample
>> that lies in the region where two bins overlap, you could just pick
>> one. You then have the problem of non-uniqueness. If you'd picked the
>> other bin you'd have a different probability distribution function.
>> This a bad property to have.
>>
>> If you don't want to pick a neighbouring bin to apply more mass, and
>> just increase the width of the each bin's matplotlib.patches.Patch
>> object, then that is more sensible. Except now you have the problem of
>> displaying the histogram. Which bin gets displayed over its left
>> neighbour? And its right neighbour?
>>
>> I dread to think what this would imply if you also wanted to stack
>> such histograms. A potential can of worms.
>>
>
> The closest I could think of as something reasonable is to apply a
> convolution of some sort to the discrete pdf to produce an approximation of
> a continuous PDF.
>
> Cheers!
> Ben Root

Yes. That's possible. The issue here, though, is getting the discrete
case to start with. There are multiple ways to do it depending on your
choice of bin, and the result is not independent of this choice.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Re: [Matplotlib-users] Histogram with overlapping bins

[Benjamin R. <ben...@ou...>]

On Saturday, October 20, 2012, Damon McDougall wrote:

> On Sat, Oct 20, 2012 at 10:25 PM, Steven Boada <bo...@ph...<javascript:;>>
> wrote:
> > It'd be cool if we could do something like
> >
> > bins = [(0.0,0.05,0.1),(0.05,0.1,0.15)...]
> >
> > Where I have specified the left edge, center and right edge of each
> > bin. Yeah, that'd be pretty slick.
> >
> > S
> >
> > On Sat Oct 20 16:21:41 2012, Steven Boada wrote:
> >> Let's say I generate a bunch of random numbers from 0-1. Then, I'd
> >> like to make a histogram of it. But here's the clincher. I'd like my
> >> bins to overlap a bit. For example, if the first bin is from 0 - 0.1,
> >> centered on 0.05, I'd like the next (second) bin to be centered on 0.1
> >> and range from 0.05 - 0.15.
> >>
> >> So basically, I want the width of each bin to be greater than the
> >> spacing.
> >>
> >> Is this something that could be done with the histogram function? I
> >> did a couple of google searches and couldn't come up with anything
> >> meaningful. Apparently, 'rwidth' in the hist function just makes the
> >> displayed bars bigger or smaller.
> >>
> >> Any thoughts?
> >>
> >
> > --
> >
> > Steven Boada
> >
> > Doctoral Student
> > Dept of Physics and Astronomy
> > Texas A&M University
> > bo...@ph... <javascript:;>
>
> My thoughts are that this goes against everything a histogram is set
> out to do; attempt to provide a 'discretised' probability distribution
> function given a set of discrete samples. Lets say a sample lies in
> the region where two bins overlap. How do you define which bin the
> sample lies in? Both? If both, how do you define the value of the
> approximated probability distribution on a bin? You could just take
> the height of the bin, but some of the bin's mass lies in each of the
> neighbouring bins.
>
> If you don't want to apply mass to the neighbouring bins for a sample
> that lies in the region where two bins overlap, you could just pick
> one. You then have the problem of non-uniqueness. If you'd picked the
> other bin you'd have a different probability distribution function.
> This a bad property to have.
>
> If you don't want to pick a neighbouring bin to apply more mass, and
> just increase the width of the each bin's matplotlib.patches.Patch
> object, then that is more sensible. Except now you have the problem of
> displaying the histogram. Which bin gets displayed over its left
> neighbour? And its right neighbour?
>
> I dread to think what this would imply if you also wanted to stack
> such histograms. A potential can of worms.
>
>
The closest I could think of as something reasonable is to apply a
convolution of some sort to the discrete pdf to produce an approximation of
a continuous PDF.

Cheers!
Ben Root

Re: [Matplotlib-users] Histogram with overlapping bins

[Damon M. <dam...@gm...>]

On Sat, Oct 20, 2012 at 10:25 PM, Steven Boada <bo...@ph...> wrote:
> It'd be cool if we could do something like
>
> bins = [(0.0,0.05,0.1),(0.05,0.1,0.15)...]
>
> Where I have specified the left edge, center and right edge of each
> bin. Yeah, that'd be pretty slick.
>
> S
>
> On Sat Oct 20 16:21:41 2012, Steven Boada wrote:
>> Let's say I generate a bunch of random numbers from 0-1. Then, I'd
>> like to make a histogram of it. But here's the clincher. I'd like my
>> bins to overlap a bit. For example, if the first bin is from 0 - 0.1,
>> centered on 0.05, I'd like the next (second) bin to be centered on 0.1
>> and range from 0.05 - 0.15.
>>
>> So basically, I want the width of each bin to be greater than the
>> spacing.
>>
>> Is this something that could be done with the histogram function? I
>> did a couple of google searches and couldn't come up with anything
>> meaningful. Apparently, 'rwidth' in the hist function just makes the
>> displayed bars bigger or smaller.
>>
>> Any thoughts?
>>
>
> --
>
> Steven Boada
>
> Doctoral Student
> Dept of Physics and Astronomy
> Texas A&M University
> bo...@ph...

My thoughts are that this goes against everything a histogram is set
out to do; attempt to provide a 'discretised' probability distribution
function given a set of discrete samples. Lets say a sample lies in
the region where two bins overlap. How do you define which bin the
sample lies in? Both? If both, how do you define the value of the
approximated probability distribution on a bin? You could just take
the height of the bin, but some of the bin's mass lies in each of the
neighbouring bins.

If you don't want to apply mass to the neighbouring bins for a sample
that lies in the region where two bins overlap, you could just pick
one. You then have the problem of non-uniqueness. If you'd picked the
other bin you'd have a different probability distribution function.
This a bad property to have.

If you don't want to pick a neighbouring bin to apply more mass, and
just increase the width of the each bin's matplotlib.patches.Patch
object, then that is more sensible. Except now you have the problem of
displaying the histogram. Which bin gets displayed over its left
neighbour? And its right neighbour?

I dread to think what this would imply if you also wanted to stack
such histograms. A potential can of worms.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Re: [Matplotlib-users] Histogram with overlapping bins

[Steven B. <bo...@ph...>]

It'd be cool if we could do something like

bins = [(0.0,0.05,0.1),(0.05,0.1,0.15)...]

Where I have specified the left edge, center and right edge of each 
bin. Yeah, that'd be pretty slick.

S

On Sat Oct 20 16:21:41 2012, Steven Boada wrote:
> Let's say I generate a bunch of random numbers from 0-1. Then, I'd
> like to make a histogram of it. But here's the clincher. I'd like my
> bins to overlap a bit. For example, if the first bin is from 0 - 0.1,
> centered on 0.05, I'd like the next (second) bin to be centered on 0.1
> and range from 0.05 - 0.15.
>
> So basically, I want the width of each bin to be greater than the
> spacing.
>
> Is this something that could be done with the histogram function? I
> did a couple of google searches and couldn't come up with anything
> meaningful. Apparently, 'rwidth' in the hist function just makes the
> displayed bars bigger or smaller.
>
> Any thoughts?
>

--

Steven Boada

Doctoral Student
Dept of Physics and Astronomy
Texas A&M University
bo...@ph...

[Matplotlib-users] Histogram with overlapping bins

[Steven B. <bo...@ph...>]

Let's say I generate a bunch of random numbers from 0-1. Then, I'd like 
to make a histogram of it. But here's the clincher. I'd like my bins to 
overlap a bit. For example, if the first bin is from 0 - 0.1, centered 
on 0.05, I'd like the next (second) bin to be centered on 0.1 and range 
from 0.05 - 0.15.

So basically, I want the width of each bin to be greater than the spacing.

Is this something that could be done with the histogram function? I did 
a couple of google searches and couldn't come up with anything 
meaningful. Apparently, 'rwidth' in the hist function just makes the 
displayed bars bigger or smaller.

Any thoughts?

-- 

Steven Boada

Doctoral Student
Dept of Physics and Astronomy
Texas A&M University
bo...@ph...

Re: [Matplotlib-users] plot with marker color coded according to z-value

[elmar w. <el...@ne...>]

Am 19.10.2012 23:26, schrieb Damon McDougall:
> Correct me if I'm wrong, but I don't even think you need them. I think
> the default cmap behaviour is to normalise to the min and max of the
> data.

yes, default cmap behaviour will normalise to the min and max of the
data.

Re: [Matplotlib-users] plot with marker color coded according to z-value

[Damon M. <dam...@gm...>]

On Fri, Oct 19, 2012 at 10:23 PM, Daπid <dav...@gm...> wrote:
> On Fri, Oct 19, 2012 at 11:08 PM, elmar werling <el...@ne...> wrote:
>> vmin=min(z), vmax=max(z)
>
> A suggestion, when dealing with arrays, it is generally faster to use
> the numpy function to compute the max and min, either np.max(z) or
> z.max(), than the standard Python one.

Correct me if I'm wrong, but I don't even think you need them. I think
the default cmap behaviour is to normalise to the min and max of the
data.

-- 
Damon McDougall
http://www.damon-is-a-geek.com
B2.39
Mathematics Institute
University of Warwick
Coventry
West Midlands
CV4 7AL
United Kingdom

Re: [Matplotlib-users] plot with marker color coded according to z-value

[Daπid <dav...@gm...>]

On Fri, Oct 19, 2012 at 11:08 PM, elmar werling <el...@ne...> wrote:
> vmin=min(z), vmax=max(z)

A suggestion, when dealing with arrays, it is generally faster to use
the numpy function to compute the max and min, either np.max(z) or
z.max(), than the standard Python one.

Re: [Matplotlib-users] plot with marker color coded according to z-value

[elmar w. <el...@ne...>]

thanks for help,

finally I found the following solution

elmar


import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt

N = 200
x = np.linspace(0,1,N)
y = np.random.randn(N)
z = np.random.randn(N)*2+5

cm = mpl.cm.get_cmap('RdYlBu')
sc = plt.scatter(x, y, c=z, vmin=min(z), vmax=max(z), s=35, cmap=cm)
plt.colorbar(sc)

plt.show()



Am 19.10.2012 21:59, schrieb Joe Kington:
>      plt.scatter(x, y, c=z, marker='s')
>      plt.colorbar()

Re: [Matplotlib-users] plot with marker color coded according to z-value

[Joe K. <jki...@wi...>]

That's what ``scatter`` is intended for.

Basically, you want something like:

    plt.scatter(x, y, c=z, marker='s')
    plt.colorbar()

Note that you can also vary the markers by size based on an additional
parameter, as well.

Have a look at this example:
http://matplotlib.org/examples/pylab_examples/scatter_demo.html

Hope that helps,
-Joe


On Fri, Oct 19, 2012 at 2:19 PM, elmar werling <el...@ne...> wrote:

> Hi,
>
> is there a way to adjust the marker color in a xy-plot in relation to
> the value of a third parameter. Something as the following - not working
> - example 1.
>
> Example 2 is working but rather slow for large arrays.
>
> cheers
> Elmar
>
>
>
>
> # example 1
>
> import matplotlib.pyplot as plt
>
> x = [1,2,3,4]
> y = x
> c = ((1.0, 0.0, 0.0), (0.8, 0.1, 0.1), (0.6, 0.2, 0.6), (0.4, 0.3, 0.3))
>
> plt.plot(x,y, color=c, marker='s')
> plt.show()
>
>
> example 2:
>
> import matplotlib.pyplot as plt
>
> x = [1,2,3,4]
> y = x
> c = ((1.0, 0.0, 0.0), (0.8, 0.1, 0.1), (0.6, 0.2, 0.6), (0.4, 0.3, 0.3))
>
> for i in range(len(x)):
>      plt.plot(x[i], y[i], color=c[i], marker='s')
>
> plt.show()
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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> _______________________________________________
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> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

[Matplotlib-users] plot with marker color coded according to z-value

[elmar w. <el...@ne...>]

Hi,

is there a way to adjust the marker color in a xy-plot in relation to 
the value of a third parameter. Something as the following - not working 
- example 1.

Example 2 is working but rather slow for large arrays.

cheers
Elmar




# example 1

import matplotlib.pyplot as plt

x = [1,2,3,4]
y = x
c = ((1.0, 0.0, 0.0), (0.8, 0.1, 0.1), (0.6, 0.2, 0.6), (0.4, 0.3, 0.3))

plt.plot(x,y, color=c, marker='s')
plt.show()


example 2:

import matplotlib.pyplot as plt

x = [1,2,3,4]
y = x
c = ((1.0, 0.0, 0.0), (0.8, 0.1, 0.1), (0.6, 0.2, 0.6), (0.4, 0.3, 0.3))

for i in range(len(x)):
     plt.plot(x[i], y[i], color=c[i], marker='s')

plt.show()

Re: [Matplotlib-users] Reading a remote JPG URL using imread

[Phil E. <pel...@gm...>]

Good idea. If the png version works then the jpg version should also be
made to work,

Would you be willing to open up an issue for the feature request? :
https://github.com/matplotlib/matplotlib/issues/new

If your ready and willing to implement such a thing, that would be even
better (just open a pull request and we can start reviewing)!

All the best,

Phil



On 19 October 2012 15:59, Rich Signell <rsi...@us...> wrote:

> MPL folks,
>
> Would it be possible to enhance Matplotlib to allow "im=imread(url)"
> to work if url returns a JPG?
>
> Currently (it seems):
>
> 1. If the URL returns a PNG this works:
>
> im = imread(urllib2.urlopen(url))
>
> 2. If the URL returns a JPG, this DOESN'T work:
>
> im = imread(urllib2.urlopen(url))
>
> .. and neither does this:
> im = imread(urllib2.urlopen(url),format='jpg')
>
> ... but this DOES work:
>
> im = Image.open(cStringIO.StringIO(urllib.urlopen(url).read()))
>
> See an example in Ipython Notebook here:
> http://nbviewer.ipython.org/3918576/
>
> So could just be hidden from the user so that "im = imread(url)" would
> just work for JPG (assuming PIL was installed)?
>
> Thanks,
> Rich
> --
> Dr. Richard P. Signell
> USGS, 384 Woods Hole Rd.
> Woods Hole, MA 02543-1598
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Re: [Matplotlib-users] dpi

[Pierre H. <pie...@cr...>]

Hi,

Le 19/10/2012 06:48, Jae-Joon Lee a écrit :
> Figuring out the dpi of the screen, I have no clue at this moment.
> Maybe this is something a gui expert can answer.
I'm certainly not a gui expert, but as a PyQt user, I know screen
resolution is indeed Python-accessible with PyQt. (I guess other
toolkits provide their own methods)

I've made a quick script that prints the screen X and Y resolution
(requires PyQt). Reference links to PyQt API docs are included.


In my case, it's 96 dpi, and that what I use in my matplotlibrc file for
the "figure.dpi" property. But I use a higher value (say 150) for
"savefig.dpi" so that I get better resolution when saving PNG images.

I agree with Nikolaus that the dpi value for displaying figures would be
better get by the software, if possible. Maybe a property like
figure.dpi='auto' should activate such a behavior. But this would
require many code duplicates, one for each gui toolkit.


Best,
Pierre

[Matplotlib-users] Reading a remote JPG URL using imread

[Rich S. <rsi...@us...>]

MPL folks,

Would it be possible to enhance Matplotlib to allow "im=imread(url)"
to work if url returns a JPG?

Currently (it seems):

1. If the URL returns a PNG this works:

im = imread(urllib2.urlopen(url))

2. If the URL returns a JPG, this DOESN'T work:

im = imread(urllib2.urlopen(url))

.. and neither does this:
im = imread(urllib2.urlopen(url),format='jpg')

... but this DOES work:

im = Image.open(cStringIO.StringIO(urllib.urlopen(url).read()))

See an example in Ipython Notebook here:
http://nbviewer.ipython.org/3918576/

So could just be hidden from the user so that "im = imread(url)" would
just work for JPG (assuming PIL was installed)?

Thanks,
Rich
-- 
Dr. Richard P. Signell
USGS, 384 Woods Hole Rd.
Woods Hole, MA 02543-1598