Re: [Matplotlib-users] How to Reduce White Space Around Figure?
On Oct 25, 2010, at 12:56 PM, Lorenzo Isella wrote: Dear All, I am aware that this question has already been asked several times on the mailing list, see e.g. http://bit.ly/aPzQTA However, in the following snippet, nothing I tried has been able to reduce the amount of white space around the figure (including toying around with ax = plt.axes([0.0, 0.0, 1.0, 1.0]) ) Of course, one can always resort to pdfcrop, but I believe there must be a better solution to resize the margins from matplotlib. Please see the snippet at the end of the email. Every suggestion is welcome. Cheers Lorenzo [cut out code snippet] You can always use subplots_adjust. I haven't looked into the details of your code, but it appears as though the actual plot (the actual graphics) is well within the margins of your subplot (extending the boundaries of the subplot would still leave a lot of white space). To counteract this you can use negative padding (and padding greater than 1); e.g. subplots_adjust(top=1, bottom=-0.2, left=-0.3, right=1.3) (you can add this right before savefig.) This means that the actual boundaries of the subplot extend outside the figure (which normally have extents from 0 to 1). The above gives pretty good results. To get any better, I think you need to adjust the aspect ratio of the figure to match the plot (you can do this by creating a figure and passing a value for figsize). -Tony P.S. since you posted code, I'll offer an unsolicited suggestion. :) You can replace all your annotate commands (except for the last 2) with two short loops: for y in np.arange(-1.4, 1.5, 0.2): annotate(, xy=(-pi/2., y), xytext=(-ini, y), arrowprops=dict(fc=g)) for y in np.arange(-1.4, 1.5, 0.2): annotate(, xy=(pi/2., y), xytext=(ini, y), arrowprops=dict(fc=g)) -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Graph
On Oct 8, 2010, at 6:52 AM, Waléria Antunes David wrote:
I don't understand what you did, i'm reading error data from a file.
def gera_grafico(N=200, eps=1):
x = np.abs(np.random.randn(N))
y = 10*np.log((30*x + 1.)**(0.5)) + 34 + eps * np.random.randn(N)
yerr = eps * np.random.randn(N)
I don't understand what you did in this code
??
Thanks,
Waleria.
Hey Waleria,
That was just some code to make up fake data with roughly the same shape and
range as the data you plotted. As I mentioned, I needed to put something there
to run your code.
Where do you get an error? If it's from the code above, you can just replace it
with your data. In any case, you don't need to use the code I pasted; just make
the changes I suggested: Fix the number passed to majorLocator and remove (or
fix the initialization of) majorFormatter.
-T
On Thu, Oct 7, 2010 at 5:06 PM, Tony S Yu tsy...@gmail.com wrote:
On Oct 7, 2010, at 3:38 PM, Waléria Antunes David wrote:
Hi,
I did like the links below, but seeing as it was my chart.
See
My code: http://pastebin.com/KcjHAPLN
On Thu, Oct 7, 2010 at 3:08 PM, John Hunter jdh2...@gmail.com wrote:
On Thu, Oct 7, 2010 at 1:01 PM, Waléria Antunes David
waleriantu...@gmail.com wrote:
I need to know how do these vertical lines on the graph. See the picture,
the lines circled.
We call these major and minor ticks. The major ticks are the taller
ones, the minor ticks are the smaller ones. Their location is
controlled by the major and minor Locator instances, and the text
printed beside them is controlled by the major and minor formatter.
See
http://matplotlib.sourceforge.net/examples/pylab_examples/major_minor_demo1.html
http://matplotlib.sourceforge.net/examples/pylab_examples/major_minor_demo2.html
and
http://matplotlib.sourceforge.net/search.html?q=codex+set_minor_locator
To control the tick properties themselves, see the Tick section in
http://matplotlib.sourceforge.net/users/artists.html
JDH
graph.png
As John mentioned, the major and minor ticks were the taller and shorter
ticks, respectively. In your pasted example, you only change the minor ticks;
by setting the majorLocator to same value as in the original example (i.e.
20), you only get the major tick at 0 because your data only goes to 1.5
(i.e. 20 is outside your plot range).
Also, the majorFormatter in the example is set to work with integers, but
your major tick labels should be float values (since most of them are between
0 and 1). Thus, the majorFormatter code is unnecessary (commented out below).
Finally, a pet peeve: when posting example code, please make the effort to
generate data for the plot so that others can easily run the code (see
attached).
-Tony
#---
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
def gera_grafico(N=200, eps=1):
x = np.abs(np.random.randn(N))
y = 10*np.log((30*x + 1.)**(0.5)) + 34 + eps * np.random.randn(N)
yerr = eps * np.random.randn(N)
majorLocator = MultipleLocator(0.2)
# majorFormatter = FormatStrFormatter('%d')
minorLocator = MultipleLocator(0.02)
fig, ax = plt.subplots()
plt.errorbar(x, y, yerr, fmt='ob', label='date')
plt.xlim(0.0, 1.5)
#plt.xscale('log')
#grid(True)
ax.xaxis.set_major_locator(majorLocator)
# ax.xaxis.set_major_formatter(majorFormatter)
ax.xaxis.set_minor_locator(minorLocator)
return fig
if __name__ == '__main__':
gera_grafico()
plt.show()
--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Graph
On Oct 7, 2010, at 11:54 AM, Waléria Antunes David wrote:
Hi,
I'm asking how to have only the vertical grid lines.?
And I'm trying to increase the spacing in the x direction, I used the
'ax.set_xscale (' log ')', but the points were even more confused.
Do you saw my image that sent yestarday?
Thanks,
Waleria
I have to agree with Ben that your description is a little confusing. Looking
at the plot you posted, I'm not sure what part of the plot you're interested in
reproducing. I don't see any vertical lines; do you mean the vertical layout
of the plot itself? If that's the case you can set the figure size such that it
is taller than it is wide. For example, before creating your plot you can call:
import matplotlib.pyplot as plt
plt.figure(figsize=(6, 8))
But from your original question, it sounds like you want the opposite, since a
wider plot would stretch the x-distance between data points (logspacing
stretches distances for low values, but maybe you want to stretch the distance
for all values?). In this case you could just increase the width of the figure;
for example:
plt.figure(figsize=(12, 6))
This may not fit on your screen, though. If you're working interactively (with
plt.show instead of plt.savefig) you can just resize the window to your liking.
-T
On Wed, Oct 6, 2010 at 5:10 PM, Benjamin Root ben.r...@ou.edu wrote:
On Wed, Oct 6, 2010 at 2:36 PM, Waléria Antunes David
waleriantu...@gmail.com wrote:
Benjamin,
I used the 'ax.set_xscale (' log ')', but the points were even more confused.
What I need is to increase from 0.0 to 0.2 points, 0.2 to 0.4 ... increase
the size of the graph. However I do not know if the chart is well visualized
on a monitor 20''.?
Are you trying to increase the spacing in the x direction or the y direction?
Log scaling is a standard trick to achieve this effect.
And how do I let my chart like this:
http://www.supernova.lbl.gov/PDFs/SCP2003SNeCMBClust.pdf
This graph format with vertical line on, something like that.
Are you asking how to add a vertical line to your graph, or how to have only
the vertical grid lines?
Ben Root
--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Graph
On Oct 7, 2010, at 3:38 PM, Waléria Antunes David wrote:
Hi,
I did like the links below, but seeing as it was my chart.
See
My code: http://pastebin.com/KcjHAPLN
On Thu, Oct 7, 2010 at 3:08 PM, John Hunter jdh2...@gmail.com wrote:
On Thu, Oct 7, 2010 at 1:01 PM, Waléria Antunes David
waleriantu...@gmail.com wrote:
I need to know how do these vertical lines on the graph. See the picture,
the lines circled.
We call these major and minor ticks. The major ticks are the taller
ones, the minor ticks are the smaller ones. Their location is
controlled by the major and minor Locator instances, and the text
printed beside them is controlled by the major and minor formatter.
See
http://matplotlib.sourceforge.net/examples/pylab_examples/major_minor_demo1.html
http://matplotlib.sourceforge.net/examples/pylab_examples/major_minor_demo2.html
and
http://matplotlib.sourceforge.net/search.html?q=codex+set_minor_locator
To control the tick properties themselves, see the Tick section in
http://matplotlib.sourceforge.net/users/artists.html
JDH
graph.png
As John mentioned, the major and minor ticks were the taller and shorter ticks,
respectively. In your pasted example, you only change the minor ticks; by
setting the majorLocator to same value as in the original example (i.e. 20),
you only get the major tick at 0 because your data only goes to 1.5 (i.e. 20 is
outside your plot range).
Also, the majorFormatter in the example is set to work with integers, but your
major tick labels should be float values (since most of them are between 0 and
1). Thus, the majorFormatter code is unnecessary (commented out below).
Finally, a pet peeve: when posting example code, please make the effort to
generate data for the plot so that others can easily run the code (see
attached).
-Tony
#---
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
def gera_grafico(N=200, eps=1):
x = np.abs(np.random.randn(N))
y = 10*np.log((30*x + 1.)**(0.5)) + 34 + eps * np.random.randn(N)
yerr = eps * np.random.randn(N)
majorLocator = MultipleLocator(0.2)
# majorFormatter = FormatStrFormatter('%d')
minorLocator = MultipleLocator(0.02)
fig, ax = plt.subplots()
plt.errorbar(x, y, yerr, fmt='ob', label='date')
plt.xlim(0.0, 1.5)
#plt.xscale('log')
#grid(True)
ax.xaxis.set_major_locator(majorLocator)
# ax.xaxis.set_major_formatter(majorFormatter)
ax.xaxis.set_minor_locator(minorLocator)
return fig
if __name__ == '__main__':
gera_grafico()
plt.show()
--
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] unicode minus sign glyph missing with serif fonts in macosx backend
On Oct 4, 2010, at 2:56 PM, Jouni K. Seppänen wrote: Joey Richards j...@caltech.edu writes: When I plot with the MacOSX backend using a serif font, the negative signs on the axis labels show up as the missing glyph open squares rather than minus signs. I am using matplotlib 1.0 installed from the dmg file for Python 2.6 on OSX 10.6. I'm using Python 2.6.6 installed from the python.org binary distribution. FWIW, I can't reproduce this on OS X 10.6.4, system Python 2.6.1, self-compiled trunk matplotlib, tried Vera and Times New Roman. This is probably unrelated, but I can't even use serif fonts on the MacOSX backend (it just shows up as sans-serif). I tried Times New Roman, Vera, and a Computer Modern unicode font that I normally use). In contrast, serif fonts work fine with TkAgg and Qt4Agg on my system (OS X 10.6.4, system Python 2.6.1, matplotlib trunk). -Tony -- Virtualization is moving to the mainstream and overtaking non-virtualized environment for deploying applications. Does it make network security easier or more difficult to achieve? Read this whitepaper to separate the two and get a better understanding. http://p.sf.net/sfu/hp-phase2-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] unicode minus sign glyph missing with serif fonts in macosx backend
On Oct 4, 2010, at 3:14 PM, Jouni K. Seppänen wrote: Tony S Yu tsy...@gmail.com writes: This is probably unrelated, but I can't even use serif fonts on the MacOSX backend (it just shows up as sans-serif). I tried Times New Roman, Vera, and a Computer Modern unicode font that I normally use). I noticed that I didn't really get Vera either, probably because I don't have it installed via the usual OS X way, and the MacOSX backend only uses fonts that it can find via CTFontCreateWithName or ATSFontFindFromPostScriptName, depending on the OS X version it's compiled for. Do you see these fonts in Font Book? Both Times New Roman and CMU show up in Font Book. (There's also a Bitstream Vera font there, but it's different from the one Matplotlib uses.) Like I said, this is probably a separate issue. I don't want to distract from the issue Joey raised---especially since I don't normally use the MacOSX backend. -Tony -- Virtualization is moving to the mainstream and overtaking non-virtualized environment for deploying applications. Does it make network security easier or more difficult to achieve? Read this whitepaper to separate the two and get a better understanding. http://p.sf.net/sfu/hp-phase2-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Combination of a box plot and a histogram
On Oct 4, 2010, at 4:09 PM, Friedrich Romstedt wrote: First attempt at a histogram strip chart (made up name). if-main block taken from [1] except that I've replaced uniform distributions with normal distributions. [1] http://matplotlib.sourceforge.net/examples/pylab_examples/boxplot_demo3.html import numpy as np import matplotlib.pyplot as plt from matplotlib import collections NORM_TYPES = dict(max=max, sum=sum) class BinCollection(collections.PatchCollection): def __init__(self, hist, bin_edges, x=0, width=1, cmap=plt.cm.gray_r, norm_type='max', **kwargs): yy = (bin_edges[:-1] + bin_edges[1:])/2. heights = np.diff(bin_edges) bins = [plt.Rectangle((x, y), width, h) for y, h in zip(yy, heights)] norm = NORM_TYPES[norm_type] fc = cmap(np.asarray(hist, dtype=float)/norm(hist)) super(BinCollection, self).__init__(bins, facecolors=fc, **kwargs) Is this equivalent to writing collections.PatchCollection.__init__() and what are the advantages of super()? I believe collections.PatchCollection.__init__() is equivalent. In this instance, I don't think there are advantages (or disadvantages) to using super---it's just how I'm used to writing classes. I think you can use axes.pcolor() to replace BinCollection. pcolor() just adds a collection similar to what you do now by hand for you. With appropriate arguments it should do the job. You can also look into pcolorfast() and pcolormesh(). Yes, you're right. This was actually my main question in the original post; i.e. what plotting function to start with. I'm not really sure how I overlooked pcolor(mesh) as a viable option. Thanks. def histstrip(x, positions=None, widths=None, ax=None): if ax is None: ax = plt.gca() if positions is None: positions = range(1, len(x) + 1) if widths is None: widths = np.min(np.diff(positions)) / 2. * np.ones(len(positions)) for data, x_pos, w in zip(x, positions, widths): x_pos -= w/2. hist, bin_edges = np.histogram(data) No other arguments to numpy.histogram() allowed? As I mentioned, this was just a function I hacked together. I didn't try to make it general purpose (yet). In my opinion this is too special to be added as a general matplotlib plotting feature. I'd agree that it's pretty specialized; especially since I haven't been able to find any mention of it. I'm still curious if there's a name for this type of plot if anyone out there knows. Best, -Tony Friedrich -- Virtualization is moving to the mainstream and overtaking non-virtualized environment for deploying applications. Does it make network security easier or more difficult to achieve? Read this whitepaper to separate the two and get a better understanding. http://p.sf.net/sfu/hp-phase2-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Combination of a box plot and a histogram
On Oct 4, 2010, at 4:30 PM, John Hunter wrote: On Thu, Sep 30, 2010 at 8:44 PM, Tony S Yu tsy...@gmail.com wrote: I'd like to make something in between a box plot [1] and a histogram. Each histogram would be represented by a single, tall, rectangular patch (like the box in a box plot), and the patch would be subdivided by the bin edges of the histogram. The face color of each sub-patch would replace the bar height in the histogram. If any of that actually made sense: * Does this type of plot have a name? * Is there an easy way to do this in Matplotlib? * If there isn't an easy way, what would be a good starting point? Initial ideas: 1) Use pcolor or imshow and embed this axes in a larger axes, 2) represent the sub-patches as a PolyCollection. If you don't need faceting (dark edges around the bins), imshow with the extent set would be the easiest way. If you want faceting, pcolor should work as well. Thanks! I'll give both imshow and pcolor a try. Most likely I'll use pcolor, since lighter bins would completely disappear without faceting (... or maybe that's a good thing). -Tony -- Virtualization is moving to the mainstream and overtaking non-virtualized environment for deploying applications. Does it make network security easier or more difficult to achieve? Read this whitepaper to separate the two and get a better understanding. http://p.sf.net/sfu/hp-phase2-d2d ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Combination of a box plot and a histogram
On Oct 1, 2010, at 9:40 AM, Benjamin Root wrote:On Thu, Sep 30, 2010 at 8:44 PM, Tony S Yu tsy...@gmail.com wrote:
I'd like to make something in between a box plot [1] and a histogram. Each histogram would be represented by a single, tall, rectangular patch (like the box in a box plot), and the patch would be subdivided by the bin edges of the histogram. The face color of each sub-patch would replace the bar height in the histogram.
If any of that actually made sense:
* Does this type of plot have a name?
* Is there an easy way to do this in Matplotlib?
* If there isn't an easy way, what would be a good starting point? Initial ideas: 1) Use pcolor or imshow and embed this axes in a larger axes, 2) represent the sub-patches as a PolyCollection.
Thoughts?
-Tony
[1] e.g. http://matplotlib.sourceforge.net/examples/pylab_examples/boxplot_demo.htmlTony,
I am not quite sure I understand. [snip]Or maybe something else in the gallery is more like what you want:
http://matplotlib.sourceforge.net/gallery.htmlBen Root
I've checked the gallery, but I don't see anything that appears similar. In any case, I ended up hacking together something that works. I've attached an image of what I had in mind (created with the code at the very bottom of this reply).I ended up using mpl Rectangle objects and stringing them together using a PatchCollection. Maybe there's a more efficient way to do this, but this approach worked well-enough.Best,-Tony"""First attempt at a histogram strip chart (made up name).if-main block taken from [1] except that I've replaced uniform distributionswith normal distributions.[1] http://matplotlib.sourceforge.net/examples/pylab_examples/boxplot_demo3.html"""import numpy as npimport matplotlib.pyplot as pltfrom matplotlib import collectionsNORM_TYPES = dict(max=max, sum=sum)class BinCollection(collections.PatchCollection): def __init__(self, hist, bin_edges, x=0, width=1, cmap=plt.cm.gray_r,norm_type='max', **kwargs): yy = (bin_edges[:-1] + bin_edges[1:])/2. heights = np.diff(bin_edges) bins = [plt.Rectangle((x, y), width, h) for y, h in zip(yy, heights)] norm = NORM_TYPES[norm_type] fc = cmap(np.asarray(hist, dtype=float)/norm(hist)) super(BinCollection, self).__init__(bins, facecolors=fc, **kwargs)def histstrip(x, positions=None, widths=None, ax=None): if ax is None: ax = plt.gca() if positions is None: positions = range(1, len(x) + 1) if widths is None: widths = np.min(np.diff(positions)) / 2. * np.ones(len(positions)) for data, x_pos, w in zip(x, positions, widths): x_pos -= w/2. hist, bin_edges = np.histogram(data) bins = BinCollection(hist, bin_edges, width=w, x=x_pos) ax.add_collection(bins, autolim=True) ax.set_xticks(positions) ax.autoscale_view()if __name__ == '__main__': import matplotlib.pyplot as plt import numpy as np np.random.seed(2) inc = 0.1 e1 = np.random.normal(0,1, size=(500,)) e2 = np.random.normal(0,1, size=(500,)) e3 = np.random.normal(0,1 + inc, size=(500,)) e4 = np.random.normal(0,1 + 2*inc, size=(500,)) treatments = [e1,e2,e3,e4] fig, ax = plt.subplots() pos = np.array(range(len(treatments)))+1 histstrip(treatments, ax=ax) ax.set_xlabel('treatment') ax.set_ylabel('response') fig.subplots_adjust(right=0.99,top=0.99) plt.show()--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Combination of a box plot and a histogram
I'd like to make something in between a box plot [1] and a histogram. Each histogram would be represented by a single, tall, rectangular patch (like the box in a box plot), and the patch would be subdivided by the bin edges of the histogram. The face color of each sub-patch would replace the bar height in the histogram. If any of that actually made sense: * Does this type of plot have a name? * Is there an easy way to do this in Matplotlib? * If there isn't an easy way, what would be a good starting point? Initial ideas: 1) Use pcolor or imshow and embed this axes in a larger axes, 2) represent the sub-patches as a PolyCollection. Thoughts? -Tony [1] e.g. http://matplotlib.sourceforge.net/examples/pylab_examples/boxplot_demo.html -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] axis labels clipped
On Sep 17, 2010, at 8:58 AM, Erik Janssens wrote: Hi, I'm using matplotlib in a pyqt context, as described in the book 'Matplotlib for python developers'. When the window is large enough, everything works fine, but when the window is too small part of the x-axis labels get chopped. Is there a way to prevent this ? Preferable in combination with the user being able to resize the window. Thanks a lot, Erik Hi Erik, Last I checked there was nothing automatic for adjusting the spacing around subplots. You can do so manually using ``plt.subplots_adjust`` (see for example, http://matplotlib.sourceforge.net/examples/pylab_examples/subplots_adjust.html). A while back, I wrote some functions to calculate a good set of parameters for subplots_adjust (see attached; examples in if-main block at bottom). I've been using these functions pretty regularly, and it works pretty well for my purposes. Best, -Tony Some usage notes: The function has to draw the figure a couple of times to calculate correct spacing. When redrawing the figure (e.g. when you resize the window), you'd have to re-call the function, which would redraw the figure a couple of times before drawing the final figure. That's all to say: this is a fairly slow function. If you don't have subplots (like in your example), you can call layout.tight_borders() (instead of layout.tight()), which only requires a single redraw. When I originally posted this to the developers list, the functions didn't work with the GtkAgg backend. As far as I know, this hasn't changed. It should work fine for Qt4Agg, macosx, and TkAgg backends. import numpy as np import matplotlib.pyplot as plt from matplotlib.transforms import TransformedBbox, Affine2D PAD_INCHES = 0.1 def tight(pad_inches=PAD_INCHES, h_pad_inches=None, w_pad_inches=None): Adjust subplot parameters to give specified padding. Parameters -- pad_inches : float minimum padding between the figure edge and the edges of subplots. h_pad_inches, w_pad_inches : float minimum padding (height/width) between edges of adjacent subplots. Defaults to `pad_inches`. if h_pad_inches is None: h_pad_inches = pad_inches if w_pad_inches is None: w_pad_inches = pad_inches fig = plt.gcf() tight_borders(fig, pad_inches=pad_inches) # NOTE: border padding affects subplot spacing; tighten border first tight_subplot_spacing(fig, h_pad_inches, w_pad_inches) def tight_borders(fig, pad_inches=PAD_INCHES): Stretch subplot boundaries to figure edges plus padding. # call draw to update the renderer and get accurate bboxes. fig.canvas.draw() bbox_original = fig.bbox_inches bbox_tight = _get_tightbbox(fig, pad_inches) # figure dimensions ordered like bbox.extents: x0, y0, x1, y1 lengths = np.array([bbox_original.width, bbox_original.height, bbox_original.width, bbox_original.height]) whitespace = (bbox_tight.extents - bbox_original.extents) / lengths # border padding ordered like bbox.extents: x0, y0, x1, y1 current_borders = np.array([fig.subplotpars.left, fig.subplotpars.bottom, fig.subplotpars.right, fig.subplotpars.top]) left, bottom, right, top = current_borders - whitespace fig.subplots_adjust(bottom=bottom, top=top, left=left, right=right) def _get_tightbbox(fig, pad_inches): renderer = fig.canvas.get_renderer() bbox_inches = fig.get_tightbbox(renderer) return bbox_inches.padded(pad_inches) def tight_subplot_spacing(fig, h_pad_inches, w_pad_inches): Stretch subplots so adjacent subplots are separated by given padding. # Zero hspace and wspace to make it easier to calculate the spacing. fig.subplots_adjust(hspace=0, wspace=0) fig.canvas.draw() figbox = fig.bbox_inches ax_bottom, ax_top, ax_left, ax_right = _get_grid_boundaries(fig) nrows, ncols = ax_bottom.shape subplots_height = fig.subplotpars.top - fig.subplotpars.bottom if nrows 1: h_overlap_inches = ax_top[1:] - ax_bottom[:-1] hspace_inches = h_overlap_inches.max() + h_pad_inches hspace_fig_frac = hspace_inches / figbox.height hspace = _fig_frac_to_cell_frac(hspace_fig_frac, subplots_height, nrows) fig.subplots_adjust(hspace=hspace) subplots_width = fig.subplotpars.right - fig.subplotpars.left if ncols 1: w_overlap_inches = ax_right[:,:-1] - ax_left[:,1:] wspace_inches = w_overlap_inches.max() + w_pad_inches wspace_fig_frac = wspace_inches / figbox.width wspace = _fig_frac_to_cell_frac(wspace_fig_frac, subplots_width, ncols) fig.subplots_adjust(wspace=wspace) def _get_grid_boundaries(fig): Return grid boundaries for bboxes of subplots Returns --- ax_bottom, ax_top, ax_left, ax_right : array bbox cell-boundaries of subplot grid. If
Re: [Matplotlib-users] Z channel
On Sep 16, 2010, at 12:06 PM, Daπid wrote: No, it is not. The Z channel is an aditional number per pixel that haves the information of the deepness. When you render an image you can keep this information for adding mist, without rendering again, for example. I don't know if I have been able to explain myself, my mind is not really clear today. ;-) Hi David, I'm also having a difficult time understanding what you're after. Your description sounds to me like a normal image plot or pcolor plot; for example, http://matplotlib.sourceforge.net/examples/pylab_examples/image_interp.html http://matplotlib.sourceforge.net/examples/pylab_examples/pcolor_small.html If what you're suggesting is different, then maybe you can link to a picture/plot of what you're after. (Or if you can't find anything, maybe you could draw an example of the plot). Best, -Tony On Thu, Sep 16, 2010 at 5:12 PM, Benjamin Root ben.r...@ou.edu wrote: On Thu, Sep 16, 2010 at 12:03 AM, Daπid davidmen...@gmail.com wrote: Does MPL support in any way the Z channel? If not, is there any possibility to use it? For example, to create a parallel matrix of the same dimensions of the image with the values of Z in each pixel. Thank you very much. David. David, I am not entirely certain I understand what you mean. Perhaps you are speaking of Z-order? Using the zorder kwarg in various plotting commands, I can manually control the order in which elements are rendered. When figures are saved, depending on the file format, this information can get flattened, and therefore lost, and other formats (most of the vector-based formats) maintain this information, I believe. Does that help? Ben Root -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Line plot orientation
On Sep 11, 2010, at 12:00 PM, Radek Machulka wrote: Hi Folks, I am trying to do something similar to http://matplotlib.sourceforge.net/examples/pylab_examples/scatter_hist.html, but with a line plots instead of histograms. My problem is how to set orientation of line plot if there is no 'orientation' argument (line axHisty.hist(y, bins=bins, orientation='horizontal') in the example). Thanks a lot Radek Since a line plot doesn't really have an orientation, this might be a lot simpler than you think. If I understand your question, you can just switch your x and y data to get the desired behavior. Continuing the example you link to, just remove the lines that create the histogram (last 4 lines before plt.show) and replace with normal plot commands; for example: bins = np.arange(-lim, lim + binwidth, binwidth) x_hist, _ = np.histogram(x, bins=bins) y_hist, _ = np.histogram(y, bins=bins) x_bin_centers = y_bin_centers = (bins[:-1] + bins[1:])/2. axHistx.plot(x_bin_centers, x_hist) axHisty.plot(y_hist, y_bin_centers) plt.show() The first line above marks the last line in the example script that you should keep. Note that you don't have to use histogram data (x_hist, y_hist); I only do so to simplify the example. Also, x_bin_centers and y_bin_centers are only equal because the scatter data is square. Is this what you were going for? -Tony -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Adjusting Image size
On Sep 10, 2010, at 5:27 AM, Nils Wagner wrote:
Hi all,
what is needed to save a figure when the size is given in
pixels, i.e. 1024x772 ?
The default is 800x600 pixels.
from pylab import plot, savefig
from numpy import sin,linspace,pi
x = linspace(0,2*pi,200)
plot(x,sin(x))
savefig('test')
Nils
You can try creating a figure with the correct aspect ratio and then setting a
corresponding dpi when you save:
#---
import matplotlib.pyplot as plt
import numpy as np
plt.figure(figsize=(10.24, 7.72))
x = np.linspace(0,2*np.pi,200)
plt.plot(x, np.sin(x))
plt.savefig('test', dpi=100)
#---
I had mixed results with this: I would occasionally get figures that were one
pixel smaller than desired.
Best,
-Tony
--
Automate Storage Tiering Simply
Optimize IT performance and efficiency through flexible, powerful,
automated storage tiering capabilities. View this brief to learn how
you can reduce costs and improve performance.
http://p.sf.net/sfu/dell-sfdev2dev
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Thicker Frame and Remove Part of Frame
On Sep 10, 2010, at 10:42 AM, Ted Kord wrote:
Hi
How can I:
1. make the frame of the plot thicker and
2. remove the top and right of the frame.
Thanks
Ted
There are probably a number of ways to do this (partly because spines are
relatively new). Here's one possibility:
import matplotlib.pyplot as plt
f, ax = plt.subplots()
ax.plot([0, 1])
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
ax.spines['bottom'].set_linewidth(3)
ax.spines['left'].set_linewidth(3)
plt.show()
Best,
-Tony
--
Automate Storage Tiering Simply
Optimize IT performance and efficiency through flexible, powerful,
automated storage tiering capabilities. View this brief to learn how
you can reduce costs and improve performance.
http://p.sf.net/sfu/dell-sfdev2dev
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Triangle in a graph
On Sep 9, 2010, at 10:53 AM, Bernardo Rocha wrote:
Hi everyone,
I would like to know if it is possible (I guess it is) and how can I do a
plot such as the one in the attached figure?
Could someone help me with this? I know that this one was done in gnuplot,
but I would like to use matplotlib.
Thanks in advance.
Bernardo M. R.
Hi Bernardo,
I have some functions which I use to draw slope markers (attached). There are
examples of how to use it in the if-main block at the bottom of the file. It
should be simple enough to use and works for linear and log scales.
The functions have grown sort of organically, so they're not as polished as
they could be. In particular, the handling of linear/log scales could be
refactored (probably by making slope marker a subclass of Polygon). Anyway, I
haven't gotten around to cleaning things up, but the functions are very usable
as is.
Hope that helps,
-Tony
import numpy as np
import matplotlib.pyplot as plt
def slope_marker(origin, slope, size_frac=0.1, pad_frac=0.1, ax=None,
invert=False):
Plot triangular slope marker labeled with slope.
Parameters
--
origin : (x, y)
tuple of x, y coordinates for the slope
slope : float or (rise, run)
the length of the slope triangle
size_frac : float
the fraction of the xaxis length used to determine the size of the slope
marker. Should be less than 1.
pad_frac : float
the fraction of the slope marker used to pad text labels. Should be less
than 1.
invert : bool
Normally, the slope marker is below a line for positive slopes and above
a line for negative slopes; `invert` flips the marker.
if ax is None:
ax = plt.gca()
if np.iterable(slope):
rise, run = slope
slope = float(rise) / run
else:
rise = run = None
x0, y0 = origin
xlim = ax.get_xlim()
dx_linear = size_frac * (xlim[1] - xlim[0])
dx_decades = size_frac * (np.log10(xlim[1]) - np.log10(xlim[0]))
if invert:
dx_linear = -dx_linear
dx_decades = -dx_decades
if ax.get_xscale() == 'log':
log_size = dx_decades
dx = _log_distance(x0, log_size)
x_run = _text_position(x0, log_size/2., scale='log')
x_rise = _text_position(x0+dx, dx_decades*pad_frac, scale='log')
else:
dx = dx_linear
x_run = _text_position(x0, dx/2.)
x_rise = _text_position(x0+dx, pad_frac * dx)
if ax.get_yscale() == 'log':
log_size = dx_decades * slope
dy = _log_distance(y0, log_size)
y_run = _text_position(y0, -dx_decades*slope*pad_frac, scale='log')
y_rise = _text_position(y0, log_size/2., scale='log')
else:
dy = dx_linear * slope
y_run = _text_position(y0, -(pad_frac * dy))
y_rise = _text_position(y0, dy/2.)
x_pad = pad_frac * dx
y_pad = pad_frac * dy
va = 'top' if y_pad 0 else 'bottom'
ha = 'left' if x_pad 0 else 'right'
if rise is not None:
ax.text(x_run, y_run, str(run), va=va, ha='center')
ax.text(x_rise, y_rise, str(rise), ha=ha, va='center')
else:
ax.text(x_rise, y_rise, str(slope), ha=ha, va='center')
ax.add_patch(_slope_triangle(origin, dx, dy))
def log_displace(x0, dx_log=None, x1=None, frac=None):
Return point displaced by a logarithmic value.
For example, if you want to move 1 decade away from `x0`, set `dx_log` = 1,
such that for `x0` = 10, we have `displace(10, 1)` = 100
Parameters
--
x0 : float
reference point
dx_log : float
displacement in decades.
x1 : float
end point
frac : float
fraction of line (on logarithmic scale) between x0 and x1
if dx_log is not None:
return 10**(np.log10(x0) + dx_log)
elif x1 is not None and frac is not None:
return 10**(np.log10(x0) + frac * np.log10(float(x1)/x0))
else:
raise ValueError('Specify `dx_log` or both `x1` and `frac`.')
def _log_distance(x0, dx_decades):
return log_displace(x0, dx_decades) - x0
def _text_position(x0, dx, scale='linear'):
if scale == 'linear':
return x0 + dx
elif scale == 'log':
return log_displace(x0, dx)
else:
raise ValueError('Unknown value for `scale`: %s' % scale)
def _slope_triangle(origin, dx, dy, ec='none', fc='0.8', **poly_kwargs):
Return Polygon representing slope.
/|
/ | dy
/__|
dx
verts = [np.asarray(origin)]
verts.append(verts[0] + (dx, 0))
verts.append(verts[0] + (dx, dy))
return plt.Polygon(verts, ec=ec, fc=fc, **poly_kwargs)
if __name__ == '__main__':
plt.plot([0, 2], [0, 1])
slope_marker((1, 0.4), (1, 2))
x = np.logspace(0, 2)
fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2)
ax1.loglog(x, x**0.5)
slope_marker((10, 2),
Re: [Matplotlib-users] Math fonts not working after upgrading to MPL 1.0
On Sep 8, 2010, at 11:56 AM, Jeremy Conlin wrote: I have trouble getting any symbols or any super/sub scripts to work since I upgraded to 1.0 a few months ago. I always get a message saying that some font isn't found. This occurs whenever I try to put symbols, superscripts, or subscripts in a label, or when I use a log scale (because then it MPL has to use superscripts). I have tried changing my matplotlibrc file but haven't found any combination of settings that help. To illustrate the problem, I have included three files, one python file and the other the error as captured from the output as well as my matplotlibrc file. The python file is trivial: # - import matplotlib.pyplot as pyplot pyplot.plot([1,2,3], label='$\alpha \beta$') pyplot.legend() pyplot.show() # - Can someone please help me figure out what is wrong? I'm on a Mac running 10.6, python 2.6, matplotlib 1.0, and I have TeX installed. Works on my system if you use a raw string (note ``r`` before string): pyplot.plot([1,2,3], label=r'$\alpha \beta$') Does that fix your problem? -Tony -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Math fonts not working after upgrading to MPL 1.0
On Sep 8, 2010, at 2:10 PM, Jeremy Conlin wrote: On Wed, Sep 8, 2010 at 10:42 AM, Tony S Yu tsy...@gmail.com wrote: On Sep 8, 2010, at 11:56 AM, Jeremy Conlin wrote: I have trouble getting any symbols or any super/sub scripts to work since I upgraded to 1.0 a few months ago. I always get a message saying that some font isn't found. This occurs whenever I try to put symbols, superscripts, or subscripts in a label, or when I use a log scale (because then it MPL has to use superscripts). I have tried changing my matplotlibrc file but haven't found any combination of settings that help. To illustrate the problem, I have included three files, one python file and the other the error as captured from the output as well as my matplotlibrc file. The python file is trivial: # - import matplotlib.pyplot as pyplot pyplot.plot([1,2,3], label='$\alpha \beta$') pyplot.legend() pyplot.show() # - Can someone please help me figure out what is wrong? I'm on a Mac running 10.6, python 2.6, matplotlib 1.0, and I have TeX installed. Works on my system if you use a raw string (note ``r`` before string): pyplot.plot([1,2,3], label=r'$\alpha \beta$') Does that fix your problem? Unfortunately, no. When I use a raw string, I just get *a@ instead of the expected result. See attached figure for proof. I still get a long list of errors of fonts not being found. Jeremy mathfont.pdf Hmm, that strange. All the fonts it says aren't found are fonts that should be included in the Matplotlib install. I have pretty much the same setup as you (OSX 10.6, python 2.6), although I'm on Matplotlib trunk. Is it possible your install got screwed up some how. Have you tried a clean install of Matplotlib? If that doesn't work, I'm afraid I won't be of much help, since I can't really reproduce this on my system. Maybe, someone who knows the font system better can help. Best, -Tony -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] bug? line misses points with negative coordinates
On Sep 3, 2010, at 4:33 AM, Sébastien Barthélemy wrote: Hello, While using sage [1], I got problems drawing a line: for some reason, the points with negative coordinates are not plotted (or are plotted on top of others due to an offset problem and thus I cannot see them). I can only reproduce the bug with specific data sets. I think I could track down the bug to matplotlib, which sage uses to render 2d plots. I included a sage script which generates the data set (in a pickle file), and a python script which draws the faulty line. Usage is : $ sage generate_data.sage $ python test_mpl.py I also included the pickled data, thus you don't need sage at all. I use matplotlib 1.0.0 for python 2.6 on mac os (as provided by macport). Could somebody here confirm the problem, and give me a hint about what is going on? I can confirm the issue. This appears to be a drawing bug: when I pan the drawing so that the negative data touches the edge of the axes frame, the rest of the line is drawn. So the line object is being created, but for some reason it's not being drawn correctly. The bug is really finicky: if I plot starting from the 3rd value of your data (i.e. slice xdata, ydata with [2:]), the line is drawn completely. The strange thing is that the first 100 or so data points defines the exact same point, so there's noting special about those first two points. (but this overlaying of data may be related to the bug) I've reproduced the issue on TkAgg, Qt4Agg, and MacOSX backends, so maybe the bug is in backend_bases. (Note: unlike Agg backends, MacOSX backend doesn't show line even after panning the plot) I don't really know how to debug drawing errors like this; so this is as far as can get. Best, -Tony Regards Sebastien [1] www.sagemath.org generate_data.sagetest_mpl.pytraj_mod.pickle -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] bug? line misses points with negative coordinates
On Sep 3, 2010, at 10:23 AM, Sébastien Barthélemy wrote:
CC to matplotlib-devel matplotlib-users
2010/9/3 Tony S Yu tsy...@gmail.com:
On Sep 3, 2010, at 4:33 AM, Sébastien Barthélemy wrote:
Hello,
While using sage [1], I got problems drawing a line: for some reason,
the points with negative coordinates are not plotted (or are plotted
on top of others due to an offset problem and thus I cannot see them).
I can only reproduce the bug with specific data sets.
[1] www.sagemath.org
I think I could track down the bug to matplotlib, which sage uses to
render 2d plots.
I included a sage script which generates the data set (in a pickle
file), and a python script which draws the faulty line.
Usage is :
$ sage generate_data.sage
$ python test_mpl.py
I also included the pickled data, thus you don't need sage at all.
I use matplotlib 1.0.0 for python 2.6 on mac os (as provided by macport).
Could somebody here confirm the problem, and give me a hint about what
is going on?
I can confirm the issue.
Great, thank you. I filed a bug:
https://sourceforge.net/tracker/?func=detailaid=3058804group_id=80706atid=560720
This appears to be a drawing bug: when I pan the drawing so that the
negative data touches the edge of the axes frame, the rest of the line is
drawn. So the line object is being created, but for some reason it's not
being drawn correctly.
The bug is really finicky: if I plot starting from the 3rd value of your
data (i.e. slice xdata, ydata with [2:]), the line is drawn completely. The
strange thing is that the first 100 or so data points defines the exact same
point, so there's noting special about those first two points. (but this
overlaying of data may be related to the bug)
I've reproduced the issue on TkAgg, Qt4Agg, and MacOSX backends, so maybe
the bug is in backend_bases. (Note: unlike Agg backends, MacOSX backend
doesn't show line even after panning the plot)
I don't really know how to debug drawing errors like this; so this is as far
as can get.
I'm not sure if I should respond to this email or the bug report, but since I
made the claim here, I'll correct myself here: The bug is not in the drawing
code as I had suggested.
The bug is related to path simplification. If you turn off path simplification
(e.g. plt.rc('path', simplify=False), the line is drawn in its entirety. This
also explains why the bug disappeared when I trimmed the first two points: path
simplification is triggered from data sets with atleast 128 points (your data
has 129, so trimming two points turned off path simplification).
I just wanted to correct my earlier comments.
-T
--
This SF.net Dev2Dev email is sponsored by:
Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Change default font
On Sep 1, 2010, at 5:10 PM, Ali Fessi wrote:
Hi,
is there a way to change the default font, e.g., to Times New Roman?!
I've been looking at the rcparams but it's kind of confusing.
Cheers.
Yes, but first you should make sure the font is on your system and is of the
correct type, i.e. TrueType (TTF). AND you have to make sure know the name of
it (some fonts may have names that aren't obvious). To check the name, type the
following in the python interpreter:
from matplotlib import font_manager
font_manager.findfont('Times New Roman')
If the font manager finds it, then it should return the path to a ttf file with
a similar name; otherwise, it'll return some default font (on my system
Vera.ttf).
Assuming you've got all that sorted out, you can set the default font in each
script, or in your matplotlibrc file (i.e. globally). But first note that Times
New Roman is a serif font; matplotlib uses sans-serif fonts by default (at
least on my system). So if you decide to go with Times New Roman, or another
serif font, you need to change the font family, as well. Here's some examples
1) In a script, add:
import matplotlib.pyplot as plt
plt.rc('font', family='serif')
plt.rc('font', serif='Times New Roman')
2) In your matplotlibrc file, add:
font.family: serif
font.serif: Times New Roman
Best,
-Tony
--
This SF.net Dev2Dev email is sponsored by:
Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] MPL = Location of new figure on desktop
On Aug 20, 2010, at 10:41 AM, Benjamin Root wrote: On Fri, Aug 20, 2010 at 2:18 AM, Eric Emsellem eemse...@eso.org wrote: Hi I have one very nagging issue which I would like to solve with matplotlib once and for all: this may have to do with my desktop windown manager but I couldn't find much there, so any input is welcome. When I open a new figure, the figure ALWAYS comes BELOW my current xterm (using KDE 4.3) and ALWAYS in the wrong place (top left corner where I usually put other windows). I would like some smart location for that figure so I don't have systematically to get it up and move it when I open a new figure. Is this linked to matplotlib? (this is the only application which is not managed properly in this context). I am using ipython -pylab as a working context (on opensuse 11.2). thanks and cheers Eric Eric, One possibility for this behavior might be that you might be defaulting to a different backend than QT. I would imagine if matplotlib is defaulting to the GTKAgg backend or the Tk backend, then the figure window would not behave properly in the window manager. You can set a default backend value to Qt4Agg in your matplotlibrc file. Maybe that would work. Ben Root I've had the same issue as Eric using Qt4Agg as the backend (and with all other backends I've used). As Eric mentioned, I have this windowing issue with ipython -pylab, but this issue also arises when running scripts from the command line and from my text editor (i.e. it's not ipython specific). -Tony -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] MPL = Location of new figure on desktop
On Aug 20, 2010, at 10:59 AM, Benjamin Root wrote: On Fri, Aug 20, 2010 at 9:51 AM, Tony S Yu tsy...@gmail.com wrote: On Aug 20, 2010, at 10:41 AM, Benjamin Root wrote: On Fri, Aug 20, 2010 at 2:18 AM, Eric Emsellem eemse...@eso.org wrote: Hi I have one very nagging issue which I would like to solve with matplotlib once and for all: this may have to do with my desktop windown manager but I couldn't find much there, so any input is welcome. When I open a new figure, the figure ALWAYS comes BELOW my current xterm (using KDE 4.3) and ALWAYS in the wrong place (top left corner where I usually put other windows). I would like some smart location for that figure so I don't have systematically to get it up and move it when I open a new figure. Is this linked to matplotlib? (this is the only application which is not managed properly in this context). I am using ipython -pylab as a working context (on opensuse 11.2). thanks and cheers Eric Eric, One possibility for this behavior might be that you might be defaulting to a different backend than QT. I would imagine if matplotlib is defaulting to the GTKAgg backend or the Tk backend, then the figure window would not behave properly in the window manager. You can set a default backend value to Qt4Agg in your matplotlibrc file. Maybe that would work. Ben Root I've had the same issue as Eric using Qt4Agg as the backend (and with all other backends I've used). As Eric mentioned, I have this windowing issue with ipython -pylab, but this issue also arises when running scripts from the command line and from my text editor (i.e. it's not ipython specific). -Tony Does it also happen with the QtAgg backend? Does the behavior change based on which backend you choose? That might help narrow down whether it is a problem with particular backends or with the backend interface. Ben Root A couple of corrections: 1) I wasn't clear earlier: I was agreeing with Eric on the fact that the plot window appeared below other windows. The location (e.g. top-left corner) depends on the backend I use. 2) I was wrong that all backends show up below the terminal window: the MacOSX backend creates plots above other windows (unfortunately, I can't test QtAgg; only macosx, qt4agg, and tkagg). -Tony -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] creating figures of exact size
On Aug 17, 2010, at 11:02 AM, Bala subramanian wrote:
Friends,
I am trying to make a figure for publication. I am making a double column
figure of 7inch as per journal guidelines. The figure comes out nicely but
the final size of the figure that is saved is not what i have given in
'figsize'. It is 10inch X 5.38 inch. How can i make mpl to create the figure
of exact size and resolution?
fig=plt.figure(figsize=(7,4))
fig.subplots_adjust(wspace=0.1,hspace=0.1)
ax1=fig.add_subplot(221)
ax2=fig.add_subplot(222,sharex=ax1,sharey=ax1)
ax3=fig.add_subplot(223,sharex=ax1,sharey=ax1)
ax4=fig.add_subplot(224,sharex=ax1,sharey=ax1)
Thanks,
Bala
That's strange. I don't see any problems with the figure size on my system.
This may seem like a silly question, but do you have the same sizing issue for
the following code:
import matplotlib.pyplot as plt
fig=plt.figure(figsize=(7,4))
fig.subplots_adjust(wspace=0.1,hspace=0.1)
ax1=fig.add_subplot(221)
ax2=fig.add_subplot(222,sharex=ax1,sharey=ax1)
ax3=fig.add_subplot(223,sharex=ax1,sharey=ax1)
ax4=fig.add_subplot(224,sharex=ax1,sharey=ax1)
plt.savefig('test.pdf')
# works fine on my system with png, pdf, and eps
I just want to make sure you aren't altering the figure in any other way before
you save.
Are you using savefig or are you saving from a GUI window? Are you on a current
version of matplotlib (if yes, you might be interested in `plt.subplots` to
create your axes)? What image format are you using?
-Tony
--
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Hints on sizing plot elements?
On Aug 12, 2010, at 1:08 AM, Russell E. Owen wrote:
I'm making a strip chart widget (which I plan to make publicly available
when finished). The basics are working fine, but the automatic sizing is
not doing so well. Strip charts are typically short, and when suitably
short the X axis annotations are partially truncated.
So...can I convince the automatic sizer to always show the full X (time)
axis annotations and put all the variable sizing into the data area? Or
do I have to manually set them somehow?
As far as I know, there's nothing to automatically resize the padding around
the the axes. (The manual way to do it is to call `fig.subplots_adjust`). I
wrote a helper script (attached below) to adjust the layout so that there's a
specified amount of padding around the axes.
Unfortunately, this resizer doesn't function correctly when using the GTK
backend. It apparently works fine with TkAgg, MacOSX, and Qt4Agg backends.
Also, is there a way from my software (not a .matplotlibrc file) to
globally make the default background color white for axis annotation
areas? Right now the background is gray for annotations and while for
plot area and I'd prefer it was all white.
-- Russell
Just set plt.rc('figure', facecolor='w') in your code (assuming you've imported
matplotlib.pyplot as plt).
Best,
-Tony
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.transforms import TransformedBbox, Affine2D
PAD_INCHES = 0.1
def tight_layout(pad_inches=PAD_INCHES, h_pad_inches=None, w_pad_inches=None):
Adjust subplot parameters to give specified padding.
Parameters
--
pad_inches : float
minimum padding between the figure edge and the edges of subplots.
h_pad_inches, w_pad_inches : float
minimum padding (height/width) between edges of adjacent subplots.
Defaults to `pad_inches`.
if h_pad_inches is None:
h_pad_inches = pad_inches
if w_pad_inches is None:
w_pad_inches = pad_inches
fig = plt.gcf()
tight_borders(fig, pad_inches=pad_inches)
# NOTE: border padding affects subplot spacing; tighten border first
tight_subplot_spacing(fig, h_pad_inches, w_pad_inches)
def tight_borders(fig, pad_inches=PAD_INCHES):
Stretch subplot boundaries to figure edges plus padding.
# call draw to update the renderer and get accurate bboxes.
fig.canvas.draw()
bbox_original = fig.bbox_inches
bbox_tight = _get_tightbbox(fig, pad_inches)
# figure dimensions ordered like bbox.extents: x0, y0, x1, y1
lengths = np.array([bbox_original.width, bbox_original.height,
bbox_original.width, bbox_original.height])
whitespace = (bbox_tight.extents - bbox_original.extents) / lengths
# border padding ordered like bbox.extents: x0, y0, x1, y1
current_borders = np.array([fig.subplotpars.left, fig.subplotpars.bottom,
fig.subplotpars.right, fig.subplotpars.top])
left, bottom, right, top = current_borders - whitespace
fig.subplots_adjust(bottom=bottom, top=top, left=left, right=right)
def _get_tightbbox(fig, pad_inches):
renderer = fig.canvas.get_renderer()
bbox_inches = fig.get_tightbbox(renderer)
return bbox_inches.padded(pad_inches)
def tight_subplot_spacing(fig, h_pad_inches, w_pad_inches):
Stretch subplots so adjacent subplots are separated by given padding.
# Zero hspace and wspace to make it easier to calculate the spacing.
fig.subplots_adjust(hspace=0, wspace=0)
fig.canvas.draw()
figbox = fig.bbox_inches
ax_bottom, ax_top, ax_left, ax_right = _get_grid_boundaries(fig)
nrows, ncols = ax_bottom.shape
subplots_height = fig.subplotpars.top - fig.subplotpars.bottom
if nrows 1:
h_overlap_inches = ax_top[1:] - ax_bottom[:-1]
hspace_inches = h_overlap_inches.max() + h_pad_inches
hspace_fig_frac = hspace_inches / figbox.height
hspace = _fig_frac_to_cell_frac(hspace_fig_frac, subplots_height, nrows)
fig.subplots_adjust(hspace=hspace)
subplots_width = fig.subplotpars.right - fig.subplotpars.left
if ncols 1:
w_overlap_inches = ax_right[:,:-1] - ax_left[:,1:]
wspace_inches = w_overlap_inches.max() + w_pad_inches
wspace_fig_frac = wspace_inches / figbox.width
wspace = _fig_frac_to_cell_frac(wspace_fig_frac, subplots_width, ncols)
fig.subplots_adjust(wspace=wspace)
def _get_grid_boundaries(fig):
Return grid boundaries for bboxes of subplots
Returns
---
ax_bottom, ax_top, ax_left, ax_right : array
bbox cell-boundaries of subplot grid. If a subplot spans cells, the grid
boundaries cutting through that subplot will be masked.
nrows, ncols, n = fig.axes[0].get_geometry()
# Initialize boundaries as masked arrays; in the future, support subplots
# that span multiple rows/columns, which would
Re: [Matplotlib-users] Sequential Calls to create bar charts jumbles output on second. first always ok.
On Aug 11, 2010, at 6:56 AM, Rob Schneider wrote:
I extract data out of a database (via Django and Python). I'm drawing two
bar charts. One is a stacked bar, and one is a simple bar.
The code for each graph is in their own function. I call the function to
draw the graph sequencially (in function CreateAllWebSite() below).
Problem is that when I do this, the graph called second comes out all
jumbled. See attached copies of png files. If I swap the function calls,
always first is ok and the the second one is jumbled. If I call them one at
a time, they both work just fine (which is how i developed the second). once
put together, the second is wrong. For example, the legend from the first
graph gets put on the second graph . The x-axis for the second is all jumbled
at the bottom left corner of the graph instead of along the x-axis properly.
I'm using Matplotlib 0.98.5.3 on OS X. I will upgrade to 1.0 of Matplot lib
soon.
I suspect some sort of memory issue; perhaps caused by how I import
matplotlib in the global section of the python program; but far as I can tell
this is correct, or is it? I suspect memory as how else would legend from
the first graph get put on the second graph? Is there some sort of reset
function to call to clear out the old graph? I sort of thought that calling a
completely different function would cover that.
Here's the code extract with portions I think no relevant snipped out. From
debugging I'm confident the number arrays holding the data is ok. As I said,
when producing the graphs one at a time, it work fine. So that code snipped
out below.
#!/usr/bin/env python
# −*− coding: UTF−8 −*−
import matplotlib
matplotlib.use('Agg') # before importing pyplot per docs
import matplotlib.pyplot as plt
import numpy as np
[snipped the import of Python and Django libraries]
###
def CreateAllWebSite():
# here is the one function that calls the two graphing functions
sequentially.
# whichever of these is called first is done fine. Second flawed. calling
one at at time, each works ok
CreateMemberStatFigure()
CreateMemberStatCategoryFigure()
###
def CreateMemberStatFigure():
# this function creates a stacked bar chart
[snipped out portions where arrays created]
Hi Rob,
It would be helpful if you could provide a runnable example. I know it's a
pain, but you should simplify your example so that it's runnable with only
matplotlib and numpy You should create some fake data to replace these portions
that you've cut out. Plus there are some (Django?) classes/functions/globals
that are undefined.
Best,
-Tony
--
This SF.net email is sponsored by
Make an app they can't live without
Enter the BlackBerry Developer Challenge
http://p.sf.net/sfu/RIM-dev2dev
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] PolyCollection API
On Jul 27, 2010, at 2:14 PM, Mathew Yeates wrote: I installed matplotlib 1.0 and now I get a different error s=[0,0,8,8] ys=[0,8,8,0] verts=zip(xs,ys) poly = PolyCollection(verts) fails at line 587 in collections because xy = array([0, 0]) # xy.shape = (2,) and line 587 says xy = np.concatenate([xy, np.zeros((1,2))]) What do I do? -Mathew I don't really use PolyCollection, but the docstring suggests you need to put your verts inside of a list: *verts* is a sequence of ( *verts0*, *verts1*, ...) where *verts_i* is a sequence of *xy* tuples of vertices, or an equivalent :mod:`numpy` array of shape (*nv*, 2). It's a bit confusing, but the first argument, verts, is actually a sequence, of a sequence, of vertices (the repetition is intentional). For example: square = [(0, 0), (0, 4), (4, 4), (4, 0)] triangle = [(0, 4), (0, 7), (4, 4)] verts = [square, triangle] In other words, the verts you created in your description describes a single polygon, where as verts should be a list of polygons. -Tony -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://ad.doubleclick.net/clk;226879339;13503038;l? http://clk.atdmt.com/CRS/go/247765532/direct/01/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Case stories of software including Matplotlib
On Jul 27, 2010, at 1:31 PM, ms wrote: On 27/07/10 15:05, Benjamin Root wrote: On Tue, Jul 27, 2010 at 6:01 AM, German Ocampogeroca...@gmail.com wrote: Good morning Do you know where I could get examples of case stories about commercial or open source software that has been developed using the Matplotlib library? Many Thanks German German, Interesting idea. Might be something nice to add to the project page, maybe? I have no ready case story about it, but I developed and published a MPL-based open source software here: http://code.google.com/p/hooke which has been presented in a peer-reviewed academic publication on Bioinformatics ( http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp180?ijkey=B9QGeobopuepKnZkeytype=ref ) If you need information to build a case story, ask me -perhaps I can help you if it's not too much work. cheers, M. German, You might be interested in CellProfiler Analyst (http://www.cellprofiler.org/). Also, matplotlib is an optional dependency for FiPy (http://www.ctcms.nist.gov/fipy/). Best, -Tony-- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://ad.doubleclick.net/clk;226879339;13503038;l? http://clk.atdmt.com/CRS/go/247765532/direct/01/___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] sizing shapes on a plot to match axis units, not graphic points
On Jun 7, 2010, at 11:16 AM, Ian Stokes-Rees wrote:I'm generating a plot of NxN squares, where the size of the squarecorresponds to the correlation between the (i,j) point. Every (i,i)point equals 1.0. I'm using "scatter" to do this, but the sizingappears to be in "points" from the graphic, rather than "units" of thetwo axes. Is there some way to account for this, or is there somebetter way to generate this image?# result = n x n matrix of correlations between points (i,j)a = arange(n).repeat(n).reshape(n,n)b = a.transpose()scatter(a.flatten(), b.flatten(), s=result, marker='s')You can see an example here, where N=300: (note, this is a 2.5 MB image):http://abitibi.sbgrid.org/se/data/shared/biodb/scop-class/a/39/1/5/.meta/tmscore2.pngThanks,IanWhat you're doing sounds very similar to a Hinton diagrom (or at least the resulting image looks similar). There's an example of plotting such a diagram in the scipy cookbook:http://www.scipy.org/Cookbook/Matplotlib/HintonDiagramsThe implementation is pretty slow because it loops through the data and draws each square one by one. I wrote a faster alternative a while back (see attached). It uses a custom PolyCollection, which uses data units for the areas instead of figure units. Also, I just noticed there's another implementation of Hinton diagrams in the matplotlib examples folder (examples/api/hinton_demo.py). For some reason, this example doesn't appear on the website, otherwise I'd link to it.I believe the difference between your plot and a hinton diagram is that you have a different metric for calculating the size of the squares.-Tonyimport numpy as np
import matplotlib.pyplot as plt
import matplotlib.collections as collections
import matplotlib.transforms as transforms
class SquareCollection(collections.RegularPolyCollection):
Return a collection of squares.
def __init__(self, **kwargs):
super(SquareCollection, self).__init__(4, rotation=np.pi/4., **kwargs)
def get_transform(self):
Return transform scaling circle areas to data space.
ax = self.axes
pts2pixels = 72.0 / ax.figure.dpi
scale_x = pts2pixels * ax.bbox.width / ax.viewLim.width
scale_y = pts2pixels * ax.bbox.height / ax.viewLim.height
return transforms.Affine2D().scale(scale_x, scale_y)
def hinton(inarray, max_weight=None):
Draw Hinton diagram for visualizing a weight matrix.
ax = plt.gca()
ax.set_axis_bgcolor('gray')
# make sure we're working with a numpy array, not a numpy matrix
inarray = np.asarray(inarray)
height, width = inarray.shape
if max_weight is None:
max_weight = 2**np.ceil(np.log(np.max(np.abs(inarray)))/np.log(2))
weights = np.clip(inarray/max_weight, -1, 1)
rows, cols = np.mgrid[:height, :width]
pos = np.where(weights 0)
neg = np.where(weights 0)
for idx, color in zip([pos, neg], ['white', 'black']):
if len(idx[0]) 0:
xy = zip(cols[idx], rows[idx])
circle_areas = np.pi / 2 * np.abs(weights[idx])
squares = SquareCollection(sizes=circle_areas,
offsets=xy, transOffset=ax.transData,
facecolor=color, edgecolor=color)
ax.add_collection(squares, autolim=True)
plt.axis('scaled')
ax.set_xlim(-0.5, width-0.5)
ax.set_ylim(height-0.5, -0.5)
ax.set_xlabel('column')
ax.set_ylabel('row')
ax.xaxis.set_ticks_position('top')
ax.xaxis.set_label_position('top')
if __name__ == '__main__':
u = lambda x: 3/4. * x**2 - 0.5 * x
A = np.array([[0, 0.5, 1], [-0.5, 0, 0.5], [-1, -0.5, 0]])
print A
hinton(A)
plt.show()
--
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] MPL uses character not defined by cmr10?
There was a recentthread about the font sizesnot matching up between regular text and math text. I decided I'd try to get matching font sizes by using computer modern as the default font, so I added the following to my matplotlibrc file:font.family: seriffont.serif: cmr10This fixes the font size issue, but for some reason, MPL's minus sign seems to be using a character not defined by the computer modern fonts (see y-axis in attached image).Is there a fix for this missing character?Best,-TonyP.S. I'm using the cmr10 fonts provided by MPL (confirmed by using the findfont function).-- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] MPL uses character not defined by cmr10?
On Apr 29, 2010, at 10:43 PM, Tony S Yu wrote: On Apr 29, 2010, at 6:09 PM, Michael Droettboom wrote: Those Computer Modern fonts (specifically the Bakoma distribution of them that matplotlib includes) use a custom character set mapping where many of the characters are in completely arbitrary locations. For regular text, matplotlib expects a regular Unicode font (particularly to get the minus sign). Since cmr10 doesn't have a standard encoding, it just won't work. Hey Mike, Thanks for your reply. That makes sense. An alternative work around (I presume) would be to install the computer modern unicode fonts (I made sure to install the ttf version). However, I'm having trouble getting MPL to find the fonts. The installed font is listed when calling `mpl.font_manager.OSXInstalledFonts()`, but it's not found when calling `mpl.font_manager.findfont` (with various names that would make sense: cmunrm, CMU Serif, etc.) Any ideas on what I'm doing wrong? Sorry, I meant to reply to the list. After clearing the fontlist cache, I was able to get this fix working. Just to summarize: * download unicode version of computer modern fonts (http://sourceforge.net/projects/cm-unicode/files/)---make sure to get the ttf version * clear out the fontlist cache (rm ~/.matplotlib/fontList.cache) * add the following to ~/matplotlib/matplotlibrc: font.family: serif font.serif: CMU Serif * alternatively, you could leave the default as sans serif and use the computer modern sans serif (unicode version): font.sans-serif: CMU Sans Serif These changes produce plots where the size of normal text matches that of mathtext. Thanks for you help, Mike! -Tony -- ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] MPL uses character not defined by cmr10?
On Apr 29, 2010, at 11:51 PM, Tony S Yu wrote:
On Apr 29, 2010, at 10:43 PM, Tony S Yu wrote:
On Apr 29, 2010, at 6:09 PM, Michael Droettboom wrote:
Those Computer Modern fonts (specifically the Bakoma distribution of them
that matplotlib includes) use a custom character set mapping where many of
the characters are in completely arbitrary locations. For regular text,
matplotlib expects a regular Unicode font (particularly to get the minus
sign). Since cmr10 doesn't have a standard encoding, it just won't work.
Hey Mike,
Thanks for your reply. That makes sense.
An alternative work around (I presume) would be to install the computer
modern unicode fonts (I made sure to install the ttf version). However, I'm
having trouble getting MPL to find the fonts.
The installed font is listed when calling
`mpl.font_manager.OSXInstalledFonts()`, but it's not found when calling
`mpl.font_manager.findfont` (with various names that would make sense:
cmunrm, CMU Serif, etc.)
Any ideas on what I'm doing wrong?
Sorry, I meant to reply to the list.
After clearing the fontlist cache, I was able to get this fix working.
Just to summarize:
* download unicode version of computer modern fonts
(http://sourceforge.net/projects/cm-unicode/files/)---make sure to get the
ttf version
* clear out the fontlist cache (rm ~/.matplotlib/fontList.cache)
* add the following to ~/matplotlib/matplotlibrc:
font.family: serif
font.serif: CMU Serif
* alternatively, you could leave the default as sans serif and use the
computer modern sans serif (unicode version):
font.sans-serif: CMU Sans Serif
These changes produce plots where the size of normal text matches that of
mathtext.
Thanks for you help, Mike!
-Tony
Umm, ... last email on this topic, I promise.
Is there any reason the font family rc parameter is case sensitive, while the
findfont input is case insensitive? In other words, replacing
font.serif: CMU Serif
with
font.serif: cmu serif
does not work. On the other hand, both of the following work:
mpl.font_manager.findfont('cmu serif')
mpl.font_manager.findfont('CMU Serif')
This caused me problems when debugging my earlier font troubles.
Best,
-Tony
--
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] custom color cycle from cmap
On Apr 8, 2010, at 8:13 AM, KrishnaPribadi wrote: Hi, I'm trying to plot a set of lines, 12 to be exact, and the default color cycle only supports 8 or 9 distinct colors. That said, I looked up the color maps and segmented it using 12 constant intervals with the hope of getting 12 distinct colors. The problem I'm running in to is that some of the line colors I get are too close to each other. This is because come shades in the colormap have a broader spectrum than others. Here is my code to set my custom default color cycle: import matplotlib as mpl cmap = mpl.cm.get_cmap(name='spectral') #I gues we can also use hsv or gist_rainbow nColors = 12 #number of colors incr = 0.9 / nColors self.mycolors = [] for i in np.arange(0,0.9,incr): self.mycolors.append(cmap(i)) you could replace the loop with a list comprehension: mycolors = [cmap(i) for i in np.arange(0,0.9,incr)] Also, arange may not be a great fit for this task; maybe linspace would work better: mycolors = [cmap(i) for i in np.linspace(0, 0.9, nColors)] This allows you to eliminate the assignment of `incr`. Note: the above colormap is different than that created by arange because linspace includes the endpoint, while arange doesn't. Hope that helps, -Tony mpl.axes.set_default_color_cycle(self.mycolors) Can anyone suggest a cleaner method? Or is there perhaps an existing class to provide distinct color lines? Thanks, Krishna -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Bug: string.letters
On Mar 9, 2010, at 1:22 PM, John Hunter wrote: On Tue, Mar 9, 2010 at 12:16 PM, Eric Firing efir...@hawaii.edu wrote: Bizarre! I can reproduce it with python 2.6 (ubuntu 9.10) and mpl from svn. I have done a little grepping and other exploration, but have completely failed to find where this change is occurring. cbook imports locale -- may be implicated: string.letters¶ The concatenation of the strings lowercase and uppercase described below. The specific value is locale-dependent, and will be updated when locale.setlocale() is called. See if simply importing locale first has the same effect. It seems to be an interaction between numpy and locale. I can reproduce the problem with: import locale import numpy as np preferredencoding = locale.getpreferredencoding() import string print string.letters The bug disappears after removing the numpy import. -Tony -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] define color cycle in matplotlibrc
Tony S Yu wrote: On Dec 29, 2009, at 3:35 AM, Dominik Szczerba wrote: Tony S Yu wrote: Hey Dominik, I'd also like to see the default color_cycle be customizeable. But, if I'm not mistaken, this approach doesn't quite do what you want (at least it doesn't on a recent version of mpl). The problem is that the color given by lines.color (rcParam) sort of overrides the first color in the specified color cycle (see ``_process_plot_var_args._clear_color_cycle`` in axes.py). It seems important for lines.color and the first color in the color cycle to match since this matching is also enforced in ``axes.set_default_color_cycle``, except in reverse (the first color in the color cycle overrides line.color). If both lines.color and axes.color_cycle (or maybe lines.color_cycle) are rcParams, there would be issues with how to match the two (e.g. which takes precedence if they differ). As I said earlier, I'd like to see this change made, but I think it may change the current behavior. Maybe a mpl developer could weigh in? -Tony Hi Tony, You are correct, line color overrides the first cycle color. That does not appear a very happy choice to me but this way or another you can still specify BOTH lines.color and the cycle in the param file to get whatever you want, no? Dominik Yup, that should do exactly what you want. But, since it's a bit of a hack (you should only need to make 1 change to matplotlibrc), I doubt this patch would be appropriate for the main distribution. Ideally, we'd need to figure out if the matplotlibrc changes 1) only lines.color and make this the first color in color_cycle, 2) only lines.color_cycle and make the first color override lines.color, or 3) both lines.color and lines.color_cycle (behavior unknown if colors don't match). Unfortunately, I don't see an easy way to tell if rcParams have been changed from their default values. Hi Tony, My patches (there were two!) remove the badly hardcoded definition of defaultColors in axes.py and instead define default axes.color_cycle in rcsetup.py (defaulting it to the already established color array ['b','g','r','c','m','y','k']). Now, in axes.py, defaultColors are taken from rcParams, and not a hardcoded array, so unless you modify your own rc file, you will get the old behavior. It is if and only if you define your color_cycle in your own rc file that will do anything new. I do not see how this introduces any incompatibilities. Dominik Sorry for the confusion. I wasn't saying your patches introduce incompatibilities, but I did say that their behavior is not ideal. For example, your matplotlibrc requires *both* lines.color_cycle : w, w, w, w, w, w (actually I think you only need one w,) *and* lines.color : w. Ideally (at least IMO), I should only need to set the color cycle, and it was surprising to me (surprises = bad) that I'd have to also set lines.color The incompatibilities I spoke of would only be true if you went with my suggestion to deprecate lines.color. -T -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] define color cycle in matplotlibrc
On Dec 24, 2009, at 4:21 AM, Dominik Szczerba wrote: OK I started hacking and added a color_cycle property to matplotlibrc. Would you be so kind to add this fix to the official version? Thanks! Dominik $ diff -w axes.py axes.py.org 135,137c135 # DSZ take defaultColors from rcParams # defaultColors = ['b','g','r','c','m','y','k'] defaultColors = rcParams['axes.color_cycle'] - --- defaultColors = ['b','g','r','c','m','y','k'] $ diff -w rcsetup.py rcsetup.py.org 442,443d441 # DSZ add color_cycle property 'axes.color_cycle' : [['b','g','r','c','m','y','k'], validate_stringlist], Add to custom matplotlibrc as e.g.: axes.color_cycle: w, w, w, w, w, w, w Hey Dominik, I'd also like to see the default color_cycle be customizeable. But, if I'm not mistaken, this approach doesn't quite do what you want (at least it doesn't on a recent version of mpl). The problem is that the color given by lines.color (rcParam) sort of overrides the first color in the specified color cycle (see ``_process_plot_var_args._clear_color_cycle`` in axes.py). It seems important for lines.color and the first color in the color cycle to match since this matching is also enforced in ``axes.set_default_color_cycle``, except in reverse (the first color in the color cycle overrides line.color). If both lines.color and axes.color_cycle (or maybe lines.color_cycle) are rcParams, there would be issues with how to match the two (e.g. which takes precedence if they differ). As I said earlier, I'd like to see this change made, but I think it may change the current behavior. Maybe a mpl developer could weigh in? -Tony -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Plotting curves filled with nonuniform color patch
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 -- 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Plotting curves filled with nonuniform color patch
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() -- 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] overriding Collections.get_transform weirdness
On Nov 12, 2009, at 8:16 AM, Michael Droettboom wrote: Thanks for looking into this further. Can you file a bug with this script that appears differently in the PDF/PS/SVG/Agg backends vs. Mac OS X? Bug filed. Thanks for your response. -Tony Cheers, Mike Tony S Yu wrote: On Nov 11, 2009, at 1:33 PM, Michael Droettboom wrote: Which older revision (or release) worked as you expected? After some digging, I think this issue is caused by an error in the macosx backend (everything works fine with tkagg, qt4agg, and agg). Oddly enough, calling savefig(), instead of show(), with the macosx backend creates the correct plot, but calling savefig() after show () does not. I'm actually not sure if my code worked for older revisions of the macosx backend (I may have had a different default backend before). The transform code doesn't work with revisions between 7950 and 7625; older versions break the macosx backend on my system (OS X 10.6.1). -Tony -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] overriding Collections.get_transform weirdness
Hi, Awhile back, Jae-Joon helped me transform collection sizes from points to data values by overriding the `get_transform` method of a RegularPolyCollection (see example code below). When I tried the code today, the collection didn't appear on the plot. Removing the get_transform method below brings the collection back, but of course, the sizes are not what I want. Some simple testing suggests that changing the transform returned by `get_transform` changes the offsets of the collection items. In other words, the transform originally (i.e. in some older revision) modified only the scale of collection items, but now appears to modify both the scale and offset. Is there a way to modify only the scale of collection items? Thanks, -Tony BTW, I'm on svn r7950. #- # The squares will not show up with the code below # Comment out the get_transform method to see squares # Change scale_x and scale_y to values close to 1 to see how they change both scale and offset class SquareCollection(collections.RegularPolyCollection): Return a collection of squares. def __init__(self, **kwargs): super(SquareCollection, self).__init__(4, rotation=np.pi/4., **kwargs) def get_transform(self): Return transform scaling circle areas to data space. ax = self.axes pts2pixels = 72.0 / ax.figure.dpi scale_x = pts2pixels * ax.bbox.width / ax.viewLim.width scale_y = pts2pixels * ax.bbox.height / ax.viewLim.height return transforms.Affine2D().scale(scale_x, scale_y) ax = plt.gca() circle_areas = np.pi * np.ones(4) xy = [(0, 0), (0, 1), (1, 0), (1, 1)] squares = SquareCollection(sizes=circle_areas, offsets=xy, transOffset=ax.transData, facecolor='black') ax.add_collection(squares, autolim=True) plt.axis([-0.5, 1.5, -0.5, 1.5]) plt.show() -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] overriding Collections.get_transform weirdness
On Nov 11, 2009, at 1:33 PM, Michael Droettboom wrote: Which older revision (or release) worked as you expected? After some digging, I think this issue is caused by an error in the macosx backend (everything works fine with tkagg, qt4agg, and agg). Oddly enough, calling savefig(), instead of show(), with the macosx backend creates the correct plot, but calling savefig() after show() does not. I'm actually not sure if my code worked for older revisions of the macosx backend (I may have had a different default backend before). The transform code doesn't work with revisions between 7950 and 7625; older versions break the macosx backend on my system (OS X 10.6.1). -Tony Mike Tony S Yu wrote: Hi, Awhile back, Jae-Joon helped me transform collection sizes from points to data values by overriding the `get_transform` method of a RegularPolyCollection (see example code below). When I tried the code today, the collection didn't appear on the plot. Removing the get_transform method below brings the collection back, but of course, the sizes are not what I want. Some simple testing suggests that changing the transform returned by `get_transform` changes the offsets of the collection items. In other words, the transform originally (i.e. in some older revision) modified only the scale of collection items, but now appears to modify both the scale and offset. Is there a way to modify only the scale of collection items? Thanks, -Tony BTW, I'm on svn r7950. #- # The squares will not show up with the code below # Comment out the get_transform method to see squares # Change scale_x and scale_y to values close to 1 to see how they change both scale and offset class SquareCollection(collections.RegularPolyCollection): Return a collection of squares. def __init__(self, **kwargs): super(SquareCollection, self).__init__(4, rotation=np.pi/ 4., **kwargs) def get_transform(self): Return transform scaling circle areas to data space. ax = self.axes pts2pixels = 72.0 / ax.figure.dpi scale_x = pts2pixels * ax.bbox.width / ax.viewLim.width scale_y = pts2pixels * ax.bbox.height / ax.viewLim.height return transforms.Affine2D().scale(scale_x, scale_y) ax = plt.gca() circle_areas = np.pi * np.ones(4) xy = [(0, 0), (0, 1), (1, 0), (1, 1)] squares = SquareCollection(sizes=circle_areas, offsets=xy, transOffset=ax.transData, facecolor='black') ax.add_collection(squares, autolim=True) plt.axis([-0.5, 1.5, -0.5, 1.5]) plt.show() -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Location matplotlibrc file on my Mac
On Nov 3, 2009, at 3:08 PM, phob...@geosyntec.com phob...@geosyntec.com wrote: -Original Message- From: Tony S Yu [mailto:ton...@mit.edu] Hi Paul, I think your matplotlibrc file should be put in: /Users/paul/.matplotlib -Tony Thanks Tony, I'll give that a shot. Shouldn't keeping it in my current working directory work as well? One of the great things about using the matplotlibrc file on my Windows machine is that I can keep different files for different projects. (Paul, I hope you don't mind if I bring this bump this back to the list). Apparently I skimmed your original email and didn't see that you tried putting the file in your working directory. That should work. (My original response is still appropriate for a global rc file.) As suggested on the mpl website (specifically: http://matplotlib.sourceforge.net/users/customizing.html ), you can try printing out the path of the rc file being used by adding the following to your script: import matplotlib print matplotlib.matplotlib_fname() Also, you may want to check that the working directory is where you think it is. For example, if you run a script from the terminal as: $ python ~/path/to/file.py Your working directory is '~' and not '~/path/to/'---so matplotlibrc file located in the same directory as file.py would not be in the working directory. Otherwise, I have no idea why the matplotlibrc is not being found in the working directory. Best, -Tony -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Location matplotlibrc file on my Mac
On Nov 3, 2009, at 1:11 PM, phob...@geosyntec.com wrote: Hey everyone, The existence of the matplotlibrc file is one reason I like MPL so much. I won't go into the convoluted work flow I had for getting my MATLAB figures completely processed in TeX, but it was nasty. On my Windows machine, I've used it with great success. But I can't get my Mac (OS 10.5) to see it at all. I've put it in my current working directory, in /Library/Frameworks/.../mpl_data, and in / Users/paul. I've confirmed that those directories are in my sys.path variable as well. Nothing seems to work. Hi Paul, I think your matplotlibrc file should be put in: /Users/paul/.matplotlib -Tony -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] polar filled plot
Hi Giovanni, Radar plots haven't been added to the core functionality of matplotlib, but there's an example of a custom radar chart class on the mpl website: http://matplotlib.sourceforge.net/examples/api/radar_chart.html Best, -Tony On Oct 17, 2009, at 9:33 AM, Giovanni Bacci wrote: Hi all. I'd like to know if it's possible to obtain a radar plot like this: http://code.google.com/intl/en/apis/chart/types.html#radar (the filled one, with cht=rs) with matplotlib. I'm using matplotlib version 0.98.5 Thanks, Giovanni -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Simple pattern recognition
On Sep 16, 2009, at 8:22 PM, Gökhan Sever wrote: Hello all, I want to be able to count predefined simple rectangle shapes on an image as shown like in this one: http://img7.imageshack.us/img7/2327/particles.png Which is in my case to count all the blue pixels (they are ice-snow flake shadows in reality) in one of the column. What is the way to automate this task, which library or technique should I study to tackle it. You should check out the ndimage subpackage in scipy. This tutorial should help you get started: http://docs.scipy.org/doc/scipy/reference/tutorial/ndimage.html The section on segmentation and labeling will be particularly useful for you. Best, -Tony -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Design questions
On Jul 30, 2009, at 5:16 PM, Gewton Jhames wrote: Anyone? On Tue, Jul 28, 2009 at 3:23 PM, Gewton Jhames gjha...@gmail.com wrote: Guys, there is the code. On Tue, Jul 28, 2009 at 3:13 PM, Gewton Jhames gjha...@gmail.com wrote: Jae-Joon Lee, savefig(file.png, bbox_inches=tight) doesn't work too. On Mon, Jul 27, 2009 at 7:00 PM, Jae-Joon Lee lee.j.j...@gmail.com wrote: [Snip] On Mon, Jul 27, 2009 at 4:06 PM, Gewton Jhamesgjha...@gmail.com wrote: On the other hand, there is some crude support for trimming, i.e., reducing the figure size while the axes area fixed. savefig(file.png, bbox_inches=tight) Note that the figure size of the saved output is only affected. This does not change the figure displayed on the screen. Regards, -JJ Jae-Joon's suggestion worked for me (using your code). Since this feature is pretty new, it may depend on the version you're using (I'm using the latest from svn). I couldn't get `autoscale_view` to work either. However, `subplots_adjust` should work with a little tweaking. Instead of the dimensions John gave, try plt.subplots_adjust(left=0.07, right=0.99). These dimensions may show up differently on your system, so try tweaking these values. Best, -T-- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Radar / Spider Chars
Josh Hemann wrote:
Tony,
I know this is a year later but your code was hugely helpful to me
last
week, so thank you
I'm glad you found it helpful.
On Jul 28, 2009, at 12:56 PM, Michael Droettboom wrote:
Would you (Josh and Tony) be amenable to us including this in the
set of
examples? It would make it easier for users to find it.
Eventually, it
might be nice to include this as a core plotting command, but in the
meantime, I think it would still be useful as-is.
Mike
Hey Mike,
I'm always happy to contribute what little I can to matplotlib.
However, if it's going to be an official example, it should be cleaned
up a bit (see attached). Summary of changes.
* My original example (i.e. not Josh's fault) didn't play well with
namespaces (i.e. from pylab import *). This has been changed to use
the proper imports (i.e. np and plt).
* Also, there were problems with rgrids when I originally wrote the
code, which has since been fixed (at least on trunk it is). This
eliminates the need to manually draw a grid.
* I made a few other clean ups for clarity. (Josh: I hope you don't
mind, I switched the data for f4_base and f5_base so that I could
remove the associated comment.)
* Final note. The polygon frame no longer works properly and I
couldn't really figure out how to fix it.
Best,
-Tony
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.projections.polar import PolarAxes
from matplotlib.projections import register_projection
def radar_factory(num_vars, frame='circle'):
Create a radar chart with `num_vars` axes.
# calculate evenly-spaced axis angles
theta = 2*np.pi * np.linspace(0, 1-1./num_vars, num_vars)
# rotate theta such that the first axis is at the top
theta += np.pi/2
def draw_poly_frame(self, x0, y0, r):
# TODO: use transforms to convert (x, y) to (r, theta)
verts = [(r*np.cos(t) + x0, r*np.sin(t) + y0) for t in theta]
return plt.Polygon(verts, closed=True, edgecolor='k')
def draw_circle_frame(self, x0, y0, r):
return plt.Circle((x0, y0), r)
frame_dict = {'polygon': draw_poly_frame, 'circle': draw_circle_frame}
if frame not in frame_dict:
raise ValueError, 'unknown value for `frame`: %s' % frame
class RadarAxes(PolarAxes):
Class for creating a radar chart (a.k.a. a spider or star chart)
http://en.wikipedia.org/wiki/Radar_chart
name = 'radar'
# use 1 line segment to connect specified points
RESOLUTION = 1
# define draw_frame method
draw_frame = frame_dict[frame]
def fill(self, *args, **kwargs):
Override fill so that line is closed by default
closed = kwargs.pop('closed', True)
return super(RadarAxes, self).fill(closed=closed, *args, **kwargs)
def plot(self, *args, **kwargs):
Override plot so that line is closed by default
lines = super(RadarAxes, self).plot(*args, **kwargs)
for line in lines:
self._close_line(line)
def _close_line(self, line):
x, y = line.get_data()
# FIXME: markers at x[0], y[0] get doubled-up
if x[0] != x[-1]:
x = np.concatenate((x, [x[0]]))
y = np.concatenate((y, [y[0]]))
line.set_data(x, y)
def set_varlabels(self, labels):
self.set_thetagrids(theta * 180/np.pi, labels)
def _gen_axes_patch(self):
x0, y0 = (0.5, 0.5)
r = 0.5
return self.draw_frame(x0, y0, r)
register_projection(RadarAxes)
return theta
if __name__ == '__main__':
#The following data is from the Denver Aerosol Sources and Health study.
#See doi:10.1016/j.atmosenv.2008.12.017
#
#The data are pollution source profile estimates for five modeled pollution
#sources (e.g., cars, wood-burning, etc) that emit 7-9 chemical species.
#The radar charts are experimented with here to see if we can nicely
#visualize how the modeled source profiles change across four scenarios:
# 1) No gas-phase species present, just seven particulate counts on
# Sulfate
# Nitrate
# Elemental Carbon (EC)
# Organic Carbon fraction 1 (OC)
# Organic Carbon fraction 2 (OC2)
# Organic Carbon fraction 3 (OC3)
# Pyrolized Organic Carbon (OP)
# 2)Inclusion of gas-phase specie carbon monoxide (CO)
# 3)Inclusion of gas-phase specie ozone (O3).
# 4)Inclusion of both gas-phase speciesis present...
N = 9
theta = radar_factory(N)
spoke_labels = ['Sulfate', 'Nitrate', 'EC', 'OC1', 'OC2', 'OC3', 'OP', 'CO',
'O3']
f1_base = [0.88, 0.01, 0.03, 0.03, 0.00, 0.06, 0.01, 0.00, 0.00]
f1_CO = [0.88, 0.02, 0.02, 0.02, 0.00, 0.05,
Re: [Matplotlib-users] Radar / Spider Chars [bug?]
On Jul 28, 2009, at 4:53 PM, Josh Hemann wrote: One small nit: I don't see any code to set the color or alpha level of the grid lines. In my example, I set the color to be a light grey because I wanted the grid lines to be seen but not be distracting from the data. Just a preference. Good point. It turns out the grid lines are already pretty faint on my computer, so I didn't need to adjust this. The most obvious thing to do is replace plt.rgrids(radial_grid) with lines, labels = plt.rgrids(radial_grid) plt.setp(lines, alpha=0.4) **However**, this modification doesn't help. In fact, nothing I did to the gridlines changed their appearance. Out of frustration, I went to the code and found that `rgrids` calls *get_ticklines* instead of *get_gridlines*. My guess is that this is a typo, but there may be a compelling reason to return the tick lines. If that's not the case, here's a ridiculously simple patch: Index: lib/matplotlib/projections/polar.py === --- lib/matplotlib/projections/polar.py (revision 7300) +++ lib/matplotlib/projections/polar.py (working copy) @@ -397,7 +397,7 @@ self._r_label2_position.clear().translate(angle, -self._rpad * rmax) for t in self.yaxis.get_ticklabels(): t.update(kwargs) -return self.yaxis.get_ticklines(), self.yaxis.get_ticklabels() +return self.yaxis.get_gridlines(), self.yaxis.get_ticklabels() set_rgrids.__doc__ = cbook.dedent(set_rgrids.__doc__) % kwdocd -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] question about setting colors of lines using colormap
Not too long ago, I posted an example of this to the list. The code near the bottom of that thread is a little more general than the one at the top and shows, three different ways to cycle through the colors of a colormap. Hope that helps, -Tony On Jul 14, 2009, at 9:51 AM, per freem wrote: Hi all, i would like to set the colors of the lines i plot (using the plot function) to go from red to blue, in evenly spaced interval. that is, imagine a color map from red to green, where i plot n-many lines, each receiving a color from this color map, starting at the red end and going to green. the docs say how to set the color cycle of lines set by plot, using: matplotlib.axes.set_default_color_cycle(['r', 'y', 'g', 'b']) but this only allows me to use named colors, and here i am looking to use shades from red to green. my question is: first, how can i generate N evenly spaced colors from the red spectrum to the green spectrum? and two, how can i make it so plot uses these colors for its line plots? thanks very much. -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] question about setting colors of lines using colormap
On Jul 14, 2009, at 3:12 PM, per freem wrote: Hi Tony, thanks for the pointer. that code does not run for me, it generates the following error: ttributeErrorTraceback (most recent call last) /Library/Python/2.5/site-packages/matplotlib/rcsetup.pyc in validate_color(s) 160 def validate_color(s): 161 'return a valid color arg' -- 162 if s.lower() == 'none': 163 return 'None' 164 if is_color_like(s): AttributeError: 'list' object has no attribute 'lower' WARNING: Failure executing file: color_cycle.py any idea what might be wrong? Hmm, it looks like there was a fix added a couple of months ago (svn revision 7164). If you're on trunk, then updating it should fix this problem. If you're not on trunk: I don't think any official releases have occurred since this fix, so I don't think updating to the last official release will help. In any case, I think this error only affects the ``cycle_cmap`` function in the code (calls to ``cmap_intervals`` should work fine). If you comment out the 4 lines of code after the comment Change the default color cycle, I believe everything should work fine. -Tony-- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Help with transforms of collections
On Jun 22, 2009, at 2:57 PM, Jae-Joon Lee wrote:
The easiest solution I can think of is doing some monkey patching.
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import numpy as np
fig = plt.figure()
ax = fig.add_subplot(111)
x = [0.25, 0.75, 0.25, 0.75]
y = [0.25, 0.25, 0.75, 0.75]
r = 0.1 * np.ones(4)
col = plt.scatter(x, y, np.pi*r**2)
from matplotlib.collections import RegularPolyCollection
class RegularPolyCollection2(RegularPolyCollection):
def get_transform(self):
ax = self.axes
sc_x = ax.bbox.width / ax.viewLim.width
sc_y = ax.bbox.height / ax.viewLim.height
return transforms.Affine2D().scale(sc_x, sc_y)
col.__class__ = RegularPolyCollection2
plt.axis('equal')
plt.show()
Thanks Jae-Joon! This is exactly what I was looking for.
-Tony
--
Are you an open source citizen? Join us for the Open Source Bridge conference!
Portland, OR, June 17-19. Two days of sessions, one day of unconference: $250.
Need another reason to go? 24-hour hacker lounge. Register today!
http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Help with transforms of collections
I'd like to plot a collection and scale the size of the collection
elements in relation to the data. My guess is that I need to use the
data transformation (ax.transData) since I would like the size of the
collection elements altered when zooming in/out.
Unfortunately, my attempt has led to weird results: the collection
offsets are shifted from the desired coordinates when using
ax.transData. Weirder still: the collection elements move *relative to
the data coordinates* when panning the figure.
I suspect that setting the collection transform to ax.transData is
somehow applying some part of the transform twice. Does anyone know
what I'm doing wrong here and how I can fix this?
Thanks!
-Tony
Attached is a toy example of what I'm trying to do. The radii of the
circles are plotted correctly, but notice the x, y coordinates don't
match the circle centers in the plot. Also, try panning the plot and
watch as the circles move relative to the tick marks.
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import numpy as np
fig = plt.figure()
ax = fig.add_subplot(111)
x = [0.25, 0.75, 0.25, 0.75]
y = [0.25, 0.25, 0.75, 0.75]
r = 0.1 * np.ones(4)
col = plt.scatter(x, y, np.pi*r**2)
pts2pixels = transforms.Affine2D().scale(72.0/fig.dpi)
col.set_transform(pts2pixels + ax.transData)
plt.axis('equal')
plt.show()
--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing
server and web deployment.
http://p.sf.net/sfu/businessobjects
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Where to post examples (specifically, one that may be useful for time-evolution plots)
On Jun 6, 2009, at 9:34 AM, John Hunter wrote:
I'm happy to post this example in the examples dir, where it will
automatically get picked up in the website gallery and examples dir.
That'd be great!
The scipy cookbook is fine too, but I would prefer that a little mini
tutorial be written in rest explaining the example and we can start a
cookbook in the mpl docs. If you would like to go this route, we can
add a section to the users guide for explained examples, aka a
cookbook.
Now that I think about it, maybe this example isn't suited for a
cookbook. Or maybe I'm just being lazy and avoiding the work involved
in writing an explanation. :P
I am curious though why you prefer to alter the default color cycle
rather than just passing the color in to the plot command -- it seems
more explicit to pass the color in directly rather than rely on the
default cycle.
JDH
Actually, I originally cycled through colors in my plot loop, which I
agree is more explicit. However, I got tired of the extra code
involved with this method and went looking for a way to change the
defaults. Plus, I already have of a module of functions I use to
change matplotlib defaults (different fontsizes, linewidths, etc. for
publications, presentations, etc), and this function fit quite nicely
with that module.
-Tony
PS. If it'd be useful to show different ways of cycling through
colors, here's another version of my example:
#!/usr/bin/env python
This example defines the function ``cycle_cmap``, which changes the default
color cycle to use color intervals from a specified colormap.
The colormap settings are predefined for a few colormaps such that colors go
from light to dark and are restricted from being too light.
These settings are particularly useful for plotting lines that evolve in time,
where there is continuous gradient from light (early times) to dark (late
times).
import matplotlib.pyplot as plt
import matplotlib as mpl
import numpy as np
REVERSE_CMAP = ['summer', 'autumn', 'winter', 'spring', 'copper']
CMAP_RANGE = dict(gray={'start':200, 'stop':0},
Blues={'start':60, 'stop':255},
Oranges={'start':60, 'stop':255},
OrRd={'start':60, 'stop':255},
BuGn={'start':60, 'stop':255},
PuRd={'start':60, 'stop':255},
YlGn={'start':60, 'stop':255},
YlGnBu={'start':60, 'stop':255},
YlOrBr={'start':60, 'stop':255},
YlOrRd={'start':60, 'stop':255},
hot={'start':230, 'stop':0},
bone={'start':200, 'stop':0},
pink={'start':160, 'stop':0})
def cmap_intervals(cmap='YlOrBr', length=50):
Return evenly spaced intervals of a given colormap `cmap`.
Colormaps listed in REVERSE_CMAP will be cycled in reverse order. Certain
colormaps have pre-specified color ranges in CMAP_RANGE. These module
variables ensure that colors cycle from light to dark and light colors are
not too close to white.
cmap - name of a matplotlib colormap (see matplotlib.pyplot.cm)
length - the number of colors used before cycling back to first color. When
`length` is large ( ~10), it is difficult to distinguish between
successive lines because successive colors are very similar.
cm = getattr(plt.cm, cmap)
if cmap in REVERSE_CMAP:
crange = dict(start=255, stop=0)
elif cmap in CMAP_RANGE:
crange = CMAP_RANGE[cmap]
else:
print '%s not in list of preset colormaps; may not be ideal' % cmap
crange = dict(start=0, stop=255)
if length abs(crange['start'] - crange['stop']):
print ('Warning: the input length is greater than the number of' +
'colors in the colormap; some colors will be repeated')
idx = np.linspace(crange['start'], crange['stop'], length).astype(np.int)
return cm(idx)
def cycle_cmap(cmap='YlOrBr', length=50):
Set default color cycle of matplotlib to a given colormap `cmap`.
The default color cycle of matplotlib is set to evenly distribute colors in
color cycle over specified colormap.
Note: this function must be called before *any* plot commands because it
changes the default color cycle.
See ``cmap_intervals`` for input details.
color_cycle = cmap_intervals(cmap, length)
# set_default_color_cycle doesn't play nice with numpy arrays
mpl.axes.set_default_color_cycle(color_cycle.tolist())
if __name__ == '__main__':
numlines = 10
x = np.linspace(0, 10)
phase_shifts = np.linspace(0, np.pi, numlines)
# Change the default color cycle
cycle_cmap(length=numlines)
plt.subplot(311)
for shift in phase_shifts:
plt.plot(x, np.sin(x - shift), linewidth=2)
# Calculate a color cycle from a cmap and pass explicitly to plot
color_cycle = cmap_intervals('summer',
[Matplotlib-users] Malloc error on show() with Wx/WxAgg
I'm running into a really bizarre error that seems to have started spontaneously (no changes I can think of were made to my system in the last few days and mpl was plotting without problems up until a few hours ago). When using WxAgg, the following code raises a malloc error. import matplotlib.pyplot as plt plt.plot([0, 1]) plt.show() Python(477,0xa0710720) malloc: *** error for object 0x220068: Non- aligned pointer being freed *** set a breakpoint in malloc_error_break to debug This error only occurs on the Wx/WxAgg backends AND when show() is called; Qt4Agg, TkAgg, and MacOSX backends work fine. This error is also generated when starting ipython with the pylab flag (and WxAgg set as the default backend). Sorry I can't give more information about the error itself; I'm not sure how to in this case. Thanks in advance for your help, -Tony Mac OS X 10.5.7 Python 2.5.1 Matplotlib trunk r7142 WX 2.8.4.0 (mac-unicode) -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Malloc error on show() with Wx/WxAgg
Correction, this error occurs on all GUI backends I've tried (I don't have gtk installed). The malloc error didn't occur on the other backends until I tried to interact with the plot window. -T On May 27, 2009, at 12:36 PM, Tony S Yu wrote: I'm running into a really bizarre error that seems to have started spontaneously (no changes I can think of were made to my system in the last few days and mpl was plotting without problems up until a few hours ago). When using WxAgg, the following code raises a malloc error. import matplotlib.pyplot as plt plt.plot([0, 1]) plt.show() Python(477,0xa0710720) malloc: *** error for object 0x220068: Non- aligned pointer being freed *** set a breakpoint in malloc_error_break to debug This error only occurs on the Wx/WxAgg backends AND when show() is called; Qt4Agg, TkAgg, and MacOSX backends work fine. This error is also generated when starting ipython with the pylab flag (and WxAgg set as the default backend). Sorry I can't give more information about the error itself; I'm not sure how to in this case. Thanks in advance for your help, -Tony Mac OS X 10.5.7 Python 2.5.1 Matplotlib trunk r7142 WX 2.8.4.0 (mac-unicode) -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Error from ``python setupegg.py develop`` using trunk
Hi,
I run mpl from the svn trunk, but I ran into a problem today after
pulling the newest version (my last update was probably a week ago).
The full build output is copied below.
I build from trunk using the following commands:
$ python setup.py build_ext --inplace
$ python setupegg.py develop
and my build failed on setupegg.py. To be honest, I'm not sure what
the second line even does, but in the past, I've run into problems
without it.
Any help would be greatly appreciated.
-Tony
=
=
=
=
BUILDING MATPLOTLIB
matplotlib: 0.98.6svn
python: 2.5.1 (r251:54863, Feb 6 2009, 19:02:12) [GCC
4.0.1 (Apple Inc. build 5465)]
platform: darwin
REQUIRED DEPENDENCIES
numpy: 1.3.0
freetype2: 9.16.3
OPTIONAL BACKEND DEPENDENCIES
libpng: 1.2.29
Tkinter: Tkinter: 50704, Tk: 8.4, Tcl: 8.4
wxPython: 2.8.4.0
* WxAgg extension not required for wxPython
= 2.8
Gtk+: no
* Building for Gtk+ requires pygtk; you must
be able
* to import gtk in your build/install
environment
Mac OS X native: yes
Qt: no
Qt4: Qt: 4.4.0, PyQt4: 4.4.2
Cairo: 1.4.12
OPTIONAL DATE/TIMEZONE DEPENDENCIES
datetime: present, version unknown
dateutil: matplotlib will provide
pytz: 2008c
OPTIONAL USETEX DEPENDENCIES
dvipng: 1.9
ghostscript: 8.57
latex: 3.141592
[Edit setup.cfg to suppress the above messages]
=
=
=
=
pymods ['pylab']
packages ['matplotlib', 'matplotlib.backends',
'matplotlib.projections', 'mpl_toolkits', 'mpl_toolkits.mplot3d',
'mpl_toolkits.axes_grid', 'matplotlib.sphinxext',
'matplotlib.numerix', 'matplotlib.numerix.mlab',
'matplotlib.numerix.ma', 'matplotlib.numerix.linear_algebra',
'matplotlib.numerix.random_array', 'matplotlib.numerix.fft',
'matplotlib.delaunay', 'dateutil', 'dateutil/zoneinfo']
running develop
running egg_info
writing lib/matplotlib.egg-info/PKG-INFO
writing namespace_packages to lib/matplotlib.egg-info/
namespace_packages.txt
writing top-level names to lib/matplotlib.egg-info/top_level.txt
writing dependency_links to lib/matplotlib.egg-info/dependency_links.txt
reading manifest template 'MANIFEST.in'
warning: no files found matching 'MANIFEST'
warning: no files found matching 'lib/mpl_toolkits'
writing manifest file 'lib/matplotlib.egg-info/SOURCES.txt'
running build_ext
building 'matplotlib.ft2font' extension
Traceback (most recent call last):
File setupegg.py, line 8, in module
{'namespace_packages' : ['mpl_toolkits']}})
File setup.py, line 267, in module
**additional_params
File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/core.py, line 151, in setup
dist.run_commands()
File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/dist.py, line 974, in run_commands
self.run_command(cmd)
File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/dist.py, line 994, in run_command
cmd_obj.run()
File /System/Library/Frameworks/Python.framework/Versions/2.5/
Extras/lib/python/setuptools/command/develop.py, line 27, in run
self.install_for_development()
File /System/Library/Frameworks/Python.framework/Versions/2.5/
Extras/lib/python/setuptools/command/develop.py, line 88, in
install_for_development
self.run_command('build_ext')
File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/cmd.py, line 333, in run_command
self.distribution.run_command(command)
File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/dist.py, line 994, in run_command
cmd_obj.run()
File /System/Library/Frameworks/Python.framework/Versions/2.5/
Extras/lib/python/setuptools/command/build_ext.py, line 46, in run
_build_ext.run(self)
File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/command/build_ext.py, line 290, in run
self.build_extensions()
File /Library/Python/2.5/site-packages/Pyrex-0.9.8.5-py2.5.egg/
Pyrex/Distutils/build_ext.py, line 82, in build_extensions
self.build_extension(ext)
File /System/Library/Frameworks/Python.framework/Versions/2.5/
Extras/lib/python/setuptools/command/build_ext.py, line 175, in
build_extension
_build_ext.build_extension(self,ext)
File /System/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/distutils/command/build_ext.py, line 453, in build_extension
sources = self.swig_sources(sources, ext)
File
Re: [Matplotlib-users] Different plot settings for different circumstances ...
On Apr 21, 2009, at 1:49 PM, Chaitanya Krishna wrote: But, anyways the point of this mail is to ask if there is a clever way of making different plots for different circumstances. For example, trying to make a plot for publication in a journal demands it being made in one way while using it in a presentation demands you to make a different one and probably trying to use it in a report requires another one. So, is there a way to decouple the plot settings (like figure size, axes properties, tick properties, etc) from the data being plotted. If so, can someone give some examples. Here's another example from the matplotlib docs that sounds more like what you're looking for: http://matplotlib.sourceforge.net/examples/pylab_examples/customize_rc.html?highlight=set_pub I use something similar to the ``set_pub`` method in the comments of the example. I have a module ``plotstyle`` which has methods for ``presentation``, ``publication``, etc. and whenever I want a script to use a certain style I just add: import plotstyle plotstyle.presention() Best, -Tony -- Stay on top of everything new and different, both inside and around Java (TM) technology - register by April 22, and save $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. 300 plus technical and hands-on sessions. Register today. Use priority code J9JMT32. http://p.sf.net/sfu/p ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] only left and bottom border in figure frame
On Feb 6, 2009, at 8:45 AM, Zunbeltz Izaola wrote:
Dear all,
I would like to have a plot where the frame only have left and
bottom border. I can not find in the documentation any function to
draw
the Rectangle contained in figure() only with this 2 lines. It is
possilbe?
Hi Zunbeltz,
Attached is an example of a custom Axes class that does what you want.
There are examples at the bottom of the file that show its use. I
worked on generalizing this idea for inclusion in MPL, but the code
got really nasty, really quickly.
On a side note, if any of the MPL devs think this would make a useful
API example (since this topic has come up a few times on the list),
feel free to do whatever you want with it.
Cheers,
-Tony
#!/usr/bin/env python
Frame classes for customizing frame borders that surround the plot axes.
import numpy as np
import matplotlib.axes as maxes
import matplotlib.pyplot as plt
import matplotlib.artist as martist
import matplotlib.collections as col
import matplotlib.projections as projections
class Frame(martist.Artist):
Draw frame along the edges of the axes patch.
Frame position can be controlled upon initialization or by setting
`positions` property with a list of positions
['left', 'right', 'top', 'bottom' | 'all']
_position_list = ('left', 'right', 'top', 'bottom')
def __init__(self, axes, positions=('left', 'bottom'), **kwargs):
`positions` is a list of strings of frame positions to plot.
['left', 'right', 'top', 'bottom' | 'all']
super(Frame, self).__init__()
# TODO: allow more keyword configuration
self.axes = axes
rc = plt.rcParams
self.color = kwargs.pop('color', rc['axes.edgecolor'])
self.linewidth = kwargs.pop('linewidth', rc['axes.linewidth'])
self.linestyle = kwargs.pop('linestyle', 'solid')
self.positions = positions
def get_data(self):
Convenience method returns tuple of (x, y) data in `self.axes`
x, y = [], []
ax = self.axes
for artist in (ax.lines, ax.patches):
if not artist == []:
x.append(np.concatenate([a.get_xdata() for a in artist]))
y.append(np.concatenate([a.get_ydata() for a in artist]))
# TODO: get scatter data from ax.collections
return (np.concatenate(x), np.concatenate(y))
def _set_frame_position(self, positions):
Set positions where frame will be drawn.
`positions` is a list of strings of frame positions to plot.
['left', 'right', 'top', 'bottom' | 'all']
self._frame_on = self._frame_dict_from(positions)
def _get_frame_position(self):
return [p for p in self._position_list if self._frame_on[p]]
# xposition tuples turn on frame for (bottom, top)
_xposition_pairs = {(True, False): 'bottom', (False, True): 'top',
(True, True): 'both', (False, False): 'none'}
def _get_xposition(self, frame_on=None):
Returns position that matches `XAxis.set_ticks_position` inputs.
`frame_on` is a dict that matches frame positions with bools.
if frame_on is None:
frame_on = self._frame_on
return self._xposition_pairs[(frame_on['bottom'], frame_on['top'])]
# yposition tuples turn on frame for (left, right)
_yposition_pairs = {(True, False): 'left', (False, True): 'right',
(True, True): 'both', (False, False): 'none'}
def _get_yposition(self, frame_on=None):
Returns position that matches `YAxis.set_ticks_position` inputs.
`frame_on` is a dict that matches frame positions with bools.
if frame_on is None:
frame_on = self._frame_on
return self._yposition_pairs[(frame_on['left'], frame_on['right'])]
def _frame_dict_from(self, positions):
Parse `positions` and return xposition, yposition tuple
`positions` is a list of strings of frame positions to plot.
['left', 'right', 'top', 'bottom' | 'all']
frame_dict = dict.fromkeys(self._position_list, False)
if 'all' in positions:
frame_dict = dict.fromkeys(self._position_list, True)
else:
for position in positions:
frame_dict[position] = True
return frame_dict
def _set_ticks(self):
Overide this method to customize tick positioning.
# Draw ticks on axes only where a frame is drawn
self.axes.xaxis.set_ticks_position(self._get_xposition())
self.axes.yaxis.set_ticks_position(self._get_yposition())
_frame_lines = dict(bottom=[(0., 0.), (1., 0.)], top=[(0., 1.), (1., 1.)],
left=[(0., 0.), (0., 1.)], right=[(1., 0.), (1., 1.)])
def _make_frame(self):
Get axis frame specified by `self._frame_on`.
lines = [self._frame_lines[p] for p in
[Matplotlib-users] GUI neutral animation example doesn't work with WxAgg/Wx
The GUI neutral animation example from the SciPy cookbook doesn't seem
to work for Wx or WxAgg backends. A plot window opens but nothing
happens. It appears to be some weird problem with ion on wx.
For example, the following code will run and immediately close:
plt.ion()
plt.plot(x, y)
plt.show()
After removing plt.ion(), a plot window is opened and the program
doesn't end until the window is closed (as expected).
If I use TkAgg or Qt4Agg (the only other GUI backends I have
installed) the examples (above and below) work as expected.
-Tony
Full Example:
#
import matplotlib
matplotlib.use('WxAgg')
import matplotlib.pyplot as plt
import numpy as np
plt.ion()
x = np.arange(0, 2*np.pi, 0.01)
line, = plt.plot(x, np.sin(x))
for i in np.arange(1, 20):
line.set_ydata(np.sin(x + i/10.0))
plt.draw()
#
PS. This seems to work the same on both trunk and 0.98.3.
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] GUI neutral animation example doesn't work with WxAgg/Wx
On Oct 23, 2008, at 12:00 PM, John Hunter wrote: On Thu, Oct 23, 2008 at 10:30 AM, Tony S Yu [EMAIL PROTECTED] wrote: The GUI neutral animation example from the SciPy cookbook doesn't seem to work for Wx or WxAgg backends. A plot window opens but nothing happens. It appears to be some weird problem with ion on wx. GUI neutral animation is not supported or recommended. I need to update the cookbook, but if you want to do it that would be great as I am short on time until next week. I'd be happy to help, but I'm not sure what had you in mind. Sorry I'm still a student---I need guidance. ;) -Tony - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Polar plot
On Sep 17, 2008, at 1:59 AM, jan gillis wrote:
Hello,
I have a problem with polar plot, if i run the following code in
matplotlib 0.98.3, polar plot is drawing a extra circle to go from
angle -3.14159265 to angle 3.03753126. Is there a solution for this
problem?
import numpy as np
from matplotlib.pyplot import figure, show, rc, grid
# radar green, solid grid lines
rc('grid', color='#316931', linewidth=1, linestyle='-')
rc('xtick', labelsize=15)
rc('ytick', labelsize=15)
# force square figure and square axes looks better for polar, IMO
fig = figure(figsize=(8,8))
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8], polar=True, axisbg='#d5de9c')
z = np.zeros((1,2000),complex)
z.real = 0.2
z.imag = np.arange(-50,50,0.05)
gamma_r = np.transpose((z-1)/(z+1))
ax.plot(np.angle(gamma_r), np.abs(gamma_r), '.-', zorder=0)
Hi Jan,
It looks like you get the circle because the angles you're plotting go
from negative to positive radians in a weird way. The circle being
drawn starts around 0 radians and goes clockwise by negative values.
Then when it gets to - pi, it switches to positive indices, i.e. pi.
Of course, these are the same points on a polar plot, but different
angles, if you want to be consistent.
Here are a couple of quick solutions, but there but there maybe better
ways of handling this.
# ~~
# get rid of the plot line above, and add the following
theta = np.angle(gamma_r)
mag = np.abs(gamma_r)
# option 1
ordered = np.argsort(theta, axis=0).squeeze()
ax.plot(theta[ordered], mag[ordered], '.-', zorder=0)
# option 2
neg_theta = np.where(theta 0)
theta[neg_theta] += 2 * np.pi
ax.plot(theta, mag, '.-', zorder=0)
# ~~
I hope that's helpful,
-Tony
ax.set_rmax(2.0)
grid(True)
show()
Kind regards,
Jean
--
Jan Gillis
Ghent University
IMEC vzw - INTEC
Sint-Pietersnieuwstraat 41
B-9000 Gent
Belgium
tel. +32 9 264 33 33
[EMAIL PROTECTED]
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK win
great prizes
Grand prize is a trip for two to an Open Source event anywhere in
the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100url=/
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Buggy 2D plot with ylim and large y values
On Sep 2, 2008, at 6:56 PM, Fredrik Johansson wrote: Hi, I've encountered what appears to be a bug in matplotlib-0.98.3 (Windows XP, Python 2.5). The following plot of a function with poles displays garbage (large filled boxes instead of a curve). There's large variation in the y values, but not so large that this shouldn't be possible to plot correctly. Is this problem known? Is there a workaround? from pylab import * x = [-2.97, -2.94, -2.91, -2.88, -2.85, -2.82, -2.79, -2.76, -2.73, -2.7, -2.67, -2.64, -2.61, -2.58, -2.55, -2.52, -2.49, -2.46, -2.43, -2.4, -2.37, -2.34, -2.31, -2.28, -2.25, -2.22, -2.19, -2.16, -2.13, -2.1, -2.07, -2.04, -2.01, -1.98, -1.95, -1.92, -1.89, -1.86, -1.83, -1.8, -1.77, -1.74, -1.71, -1.68, -1.65, -1.62, -1.59, -1.56, -1.53, -1.5, -1.47, -1.44, -1.41, -1.38, -1.35, -1.32, -1.29,-1.26, -1.23, -1.2, -1.17, -1.14, -1.11, -1.08, -1.05, -1.02, -0.99, -0.96, -0.93, -0.9, -0.87, -0.84, -0.81, -0.78, -0.75, -0.72, -0.69, -0.66, -0.63, -0.6, -0.57, -0.54, -0.51, -0.48, -0.45, -0.42, -0.39, -0.36, -0.33, -0.3, -0.27, -0.24, -0.21, -0.18, -0.15, -0.12, -0.09, -0.06, -0.03] y = [7.40742e+6, 462976.0, 91463.4, 28950.0, 11867.8, 5732.96, 3104.37, 1830.03, 1153.53, 768.963, 538.805, 395.968, 305.58, 248.666, 214.668, 197.843, 195.517, 207.33, 235.138, 283.525, 361.162, 483.641, 679.315, 1001.79, 1558.46, 2581.22, 4621.92, 9171.58, 21022.7, 60014.1, 249909.0, 2.34376e+6, 6.0e+8, 3.75e+7, 960013.0, 146498.0, 40995.2, 15633.9,7200.57, 3768.46, 2164.71, 1336.34, 875.104, 603.287, 436.34, 331.148, 264.559, 223.743, 201.613, 194.594, 201.594, 223.706, 264.503, 331.072, 436.244, 603.172, 874.968, 1336.19, 2164.53, 3768.26, 7200.35, 15633.7, 40994.9, 146498.0, 960013.0, 3.75e+7, 6.0e+8, 2.34376e+6, 249909.0, 60013.7, 21022.2, 9171.01, 4621.3, 2580.56, 1557.75, 1001.03, 678.491, 482.753, 360.205, 282.492, 234.022, 206.125, 194.213, 196.431, 213.137, 247.004, 303.774, 394.002, 536.66, 766.62, 1150.97, 1827.22, 3101.28, 5729.56, 11864.0, 28945.8, 91458.8, 462971.0, 7.40741e+6] plot(x, y) ylim([-40, 40]) show() I may be missing something here, but everything plots fine *if you remove the call to ylim*. Note that the minimum y value is 194.213. I wouldn't expect to see anything if none of the data is between y = -40 .. 40. Sorry if I'm overlooking something. Best, -Tony -- Fredrik - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Box Off on Axis
On Jul 15, 2008, at 6:17 PM, Andrea Gavana wrote:
Hi All,
I am helping my girlfriend in doing some plots for her thesis (!).
Normally, matplotlib puts the graph in a box, left y axis, bottom x
axis, right y axis, top x axis. What she would like to do is to remove
the right y axis and the top x axis, akin the matlab command box off
(if I remember correctly), leaving just the 2 principal axis in the
plot.
I remember seeing something like that done with matplotlib, but
tonight my google-fu is really bad...
Is there a way to do what she is asking me to do? ;-)
Hi Andrea,
Here's a class I wrote (see attached) to draw custom frames for
matplotlib. It defaults to the plot style you describe above. To use
the frame class, try:
import pyplot as plt
from frame import FrameAxes
plt.subplot(111, projection='frameaxes')
And then plot as you normally would. If you want an example, just run
the file directly (instead of importing).
I'm playing around with a more flexible implementation where the axes
can be placed arbitrarily (i.e. not just on the edges of the plot),
but progress has been slow because of design considerations.
Best,
-Tony
PS: note this requires Matplotlib 0.98
#!/usr/bin/env python
Frame classes for customizing frame borders that surround the plot axes.
import numpy as np
import matplotlib.axes as maxes
import matplotlib.pyplot as plt
import matplotlib.artist as martist
import matplotlib.collections as col
import matplotlib.projections as projections
class Frame(martist.Artist):
Draw frame along the edges of the axes patch.
Frame position can be controlled upon initialization or by setting
`positions` property with a list of positions
['left', 'right', 'top', 'bottom' | 'all']
_position_list = ('left', 'right', 'top', 'bottom')
def __init__(self, axes, positions=('left', 'bottom'), **kwargs):
`positions` is a list of strings of frame positions to plot.
['left', 'right', 'top', 'bottom' | 'all']
super(Frame, self).__init__()
# TODO: allow more keyword configuration
self.axes = axes
rc = plt.rcParams
self.color = kwargs.pop('color', rc['axes.edgecolor'])
self.linewidth = kwargs.pop('linewidth', rc['axes.linewidth'])
self.linestyle = kwargs.pop('linestyle', 'solid')
self.positions = positions
def get_data(self):
Convenience method returns tuple of (x, y) data in `self.axes`
x, y = [], []
ax = self.axes
for artist in (ax.lines, ax.patches):
if not artist == []:
x.append(np.concatenate([a.get_xdata() for a in artist]))
y.append(np.concatenate([a.get_ydata() for a in artist]))
# TODO: get scatter data from ax.collections
return (np.concatenate(x), np.concatenate(y))
def _set_frame_position(self, positions):
Set positions where frame will be drawn.
`positions` is a list of strings of frame positions to plot.
['left', 'right', 'top', 'bottom' | 'all']
self._frame_on = self._frame_dict_from(positions)
def _get_frame_position(self):
return [p for p in self._position_list if self._frame_on[p]]
# xposition tuples turn on frame for (bottom, top)
_xposition_pairs = {(True, False): 'bottom', (False, True): 'top',
(True, True): 'both', (False, False): 'none'}
def _get_xposition(self, frame_on=None):
Returns position that matches `XAxis.set_ticks_position` inputs.
`frame_on` is a dict that matches frame positions with bools.
if frame_on is None:
frame_on = self._frame_on
return self._xposition_pairs[(frame_on['bottom'], frame_on['top'])]
# yposition tuples turn on frame for (left, right)
_yposition_pairs = {(True, False): 'left', (False, True): 'right',
(True, True): 'both', (False, False): 'none'}
def _get_yposition(self, frame_on=None):
Returns position that matches `YAxis.set_ticks_position` inputs.
`frame_on` is a dict that matches frame positions with bools.
if frame_on is None:
frame_on = self._frame_on
return self._yposition_pairs[(frame_on['left'], frame_on['right'])]
def _frame_dict_from(self, positions):
Parse `positions` and return xposition, yposition tuple
`positions` is a list of strings of frame positions to plot.
['left', 'right', 'top', 'bottom' | 'all']
frame_dict = dict.fromkeys(self._position_list, False)
if 'all' in positions:
frame_dict = dict.fromkeys(self._position_list, True)
else:
for position in positions:
frame_dict[position] = True
return frame_dict
def _set_ticks(self):
Overide this method to customize tick positioning.
# Draw
Re: [Matplotlib-users] plotting with marker 'o' but not filled
On Jul 12, 2008, at 1:50 PM, Alan wrote:
Hi List,
I use Fink for Mac OSX, tiger 10.4.11.
So with MPL 0.90.1, this script works fine:
from matplotlib.pylab import *
import matplotlib, numpy
print matplotlib.__version, numpy.__version__
att1 = {'color': 'black', 'markerfacecolor': 'red', 'markersize':
80.0, 'markeredgewidth': 1.0, 'alpha': 1.0, 'marker': 's',
'markeredgecolor': 'blue'}
att2 = {'color': 'black', 'markerfacecolor': None, 'markersize': 8.0,
'markeredgewidth': 1.0, 'alpha': 1.0, 'marker': 'o',
'markeredgecolor': 'blue'}
plot([0],[0], **att1)
plot([0],[0], **att2)
show()
I got just a blue circle line (not filled) over a red square. However,
trying the same script with updated MPL 0.91.3, I got:
[snip]
File /sw/lib/python2.5/site-packages/matplotlib/colors.py, line
279, in to_rgb
raise ValueError('to_rgb: Invalid rgb arg %s\n%s' % (str(arg),
exc))
ValueError: to_rgb: Invalid rgb arg None
cannot convert argument to rgb sequence
Bottom line, version 0.91.3 simply doesn't like 'markerfacecolor':
None anymore.
Could you try setting 'markerfacecolor' to 'none' (Note that this is
the string, not the keyword). I'm on version 0.98.2, but I think this
worked when I was using 0.91.3. I'm not sure why this change was made,
though.
Best,
-Tony
So, is it a bug, or there's another way of getting a simple circle
not filled?
Many thanks in advance,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
-
Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW!
Studies have shown that voting for your favorite open source project,
along with a healthy diet, reduces your potential for chronic lameness
and boredom. Vote Now at http://www.sourceforge.net/community/cca08
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
-
Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW!
Studies have shown that voting for your favorite open source project,
along with a healthy diet, reduces your potential for chronic lameness
and boredom. Vote Now at http://www.sourceforge.net/community/cca08
___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] converting data between axis [0, 1] and data coordinates [min data, max data]
On Jun 30, 2008, at 11:13 AM, Michael Droettboom wrote: transScale is where all of the (optionally) logarithmic transformation takes place. I'm surprised transDesired = self.transScale + self.transLimits didn't work for going from data to a (0, 0) - (1, 1) bounding box. Can you provide a small, yet complete, example that illustrates the bug so I can look at it further? I tried to put together a simple example showing my problem, but the example worked properly! Doh! It turns out that my problem was specific to using a bounding box as an input to transform: = from numpy.random import rand import matplotlib.pyplot as plt ax = plt.subplot(111) xy = rand(5,2) ax.loglog(xy[:, 0], xy[:, 1], 'ro') trans = ax.transScale + ax.transLimits result = trans.transform(ax.dataLim) = The above command gives me: TypeError: 'Bbox' object is unsubscriptable (Note, if I call `plot` instead of `loglog` I don't have problems). The quick solution is to replace the last line with result = trans.transform(ax.dataLim._points) I guess I was confused because the transform worked fine with `plot`. Is the TypeError above expected behavior? Thanks for your help. -Tony - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] dataLim and getting the data from `scatter` (bonus: an attempt at a Frame class)
On Jun 30, 2008, at 10:10 PM, John Hunter wrote: I'd love for you to take the lead on this. Given my (and other developers) constraints on time, we'll have only limited time to help, but hopefully we can give you some pointers when you get stuck. I don't know if I'm the best person to be taking this on, but if no one else is interested, then I'd be happy to take a shot at it. Current Limitations: * the frame can only be placed on the borders of the axes (mainly because I don't know how to move the tickers anywhere else). Look at how the transforms are set in the axis.Axis class for the tickers - the ticks and labels have blended transforms which blend data coords and axes coords. That reminds me: does it make more sense to have the frame as an attribute/child of each axis (just as ticks are attributes of each axis)? It seemed more appropriate to me, but I just used the `frame` in axes because it was already defined. It would be extremely useful if you could develop and extensible API for axis handling (so one could incorporate some of these Tufte extensions and related ideas at the *user* level even if they are not built in, though we'd probably supply some by default or by example) I didn't really expect the Tufte-style frames to be incorporated into the core; Incidentally, my initial goal was just to play around with these Tufte-style frames, not to write a Frame class. Keep us posted! Will do. Thanks for your comments. -Tony- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] dataLim and getting the data from `scatter` (bonus: an attempt at a Frame class)
Hi. A couple of questions about `scatter`:Q1The bounding box `axes.dataLim` increases in size when calling scatter(x, y) compared to plot(x, y) (for the same x, y data, of course). I think this change is due to the size of the markers being added to the data limits (not sure if this is true). Is there an easy way to get the same data limits I would have for a call to `plot`?Q2Is there a way to get the data from the axes of a scatter plot?Initially I thought I could get it with:>>> for collection in ax.collections:>>> for path in collection._paths:>>> print path.verticesBut this seems to be the path that draws the scatter markers. Any ideas?Frame Class==Finally, if anyone is interested, I'm playing around with a Frame class for `axes.frame`. This class adds customizable axes frames similar to the topic of this thread:http://sourceforge.net/mailarchive/message.php?msg_id=87d57vjgye.fsf%40peds-pc311.bsd.uchicago.eduIn this older thread, the SAGE axes frames were criticized for not being flexible enough. I've tried to make this class as general as possible (within my ability:). As an example of the flexibility of this Frame class, I've added some Tufte-style frames similar to:http://hupp.org/adam/weblog/2007/09/03/etframes-applying-the-ideas-of-edward-tufte-to-matplotlib/To the developers on this thread: If there's anything I could do to make the attached Frame class more flexible (and more suitable for possible inclusion into MPL), I'd be happy to get some feedback.Current Limitations:* the frame can only be placed on the borders of the axes (mainly because I don't know how to move the tickers anywhere else).* RangeFrame only works with linear data (I'm not sure how to use the `axes.transScale`to properly transform the data)* RangeFrame and DashDotFrame don't work properly with `scatter` (because of the questions in this post).The frame class itself isn't too long, but I got a little carried away adding in extra crap.Sorry for the long, rambling email.;)-Tony#!/usr/bin/env python
Frame classes for customizing frame borders that surround the plot axes.
import numpy as np
from numpy.random import rand
import matplotlib.axes as maxes
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import matplotlib.artist as martist
import matplotlib.collections as col
import matplotlib.projections as projections
class Frame(martist.Artist):
Draw frame along the edges of the axes patch.
Frame position can be controlled upon initialization or by setting
`frame_position` property with a list of positions
['left', 'right', 'top', 'bottom' | 'all']
_position_list = ('left', 'right', 'top', 'bottom')
def __init__(self, axes, positions=('left', 'bottom'), **kwargs):
`positions` is a list of strings of frame positions to plot.
['left', 'right', 'top', 'bottom' | 'all']
super(Frame, self).__init__()
# TODO: allow more keyword configuration
self.axes = axes
rc = plt.rcParams
self.color = kwargs.pop('color', rc['axes.edgecolor'])
self.linewidth = kwargs.pop('linewidth', rc['axes.linewidth'])
self.linestyle = kwargs.pop('linestyle', 'solid')
self.frame_position = positions
def get_data(self):
Convenience method returns tuple of (x, y) data in `self.axes`
x, y = [], []
ax = self.axes
for artist in (ax.lines, ax.patches):
if not artist == []:
x.append(np.concatenate([a.get_xdata() for a in artist]))
y.append(np.concatenate([a.get_ydata() for a in artist]))
# TODO: get scatter data from ax.collections
return (np.concatenate(x), np.concatenate(y))
def _set_frame_position(self, positions):
Set positions where frame will be drawn.
`positions` is a list of strings of frame positions to plot.
['left', 'right', 'top', 'bottom' | 'all']
self._frame_on = self._frame_dict_from(positions)
def _get_frame_position(self):
return [p for p in self._position_list if self._frame_on[p]]
# xposition tuples turn on frame for (bottom, top)
_xposition_pairs = {(True, False): 'bottom', (False, True): 'top',
(True, True): 'both', (False, False): 'none'}
def _get_xposition(self, frame_on=None):
Returns position that matches `XAxis.set_ticks_position` inputs.
`frame_on` is a dict that matches frame positions with bools.
if frame_on is None:
frame_on = self._frame_on
return self._xposition_pairs[(frame_on['bottom'], frame_on['top'])]
# yposition tuples turn on frame for (left, right)
_yposition_pairs = {(True, False): 'left', (False, True): 'right',
(True, True): 'both', (False, False): 'none'}
def _get_yposition(self, frame_on=None):
Returns position that matches
Re: [Matplotlib-users] Radar / Spider Chars
I was reading through the projections docs and decided to take a shot
at creating a radar chart class. The layout of the labels and legend
is really off, but other than that, this seems to work OK. I couldn't
figure out a good way to initialize the number of axes/variables, so
there's an ugly function wrapping around the class def.
Anyway, I hope this is useful to somebody:
#!/usr/bin/env python
from matplotlib.projections.polar import PolarAxes
from matplotlib.projections import register_projection
from pylab import *
def radar_factory(num_vars, frame='polygon'):
Create a radar chart with `num_vars` axes.
# calculate evenly-spaced axis angles
theta = 2*pi * linspace(0, 1-1/float(num_vars), num_vars)
# rotate theta such that the first axis is at the top
theta += pi/2
def draw_poly_frame(self, x0, y0, r):
# TODO: should use transforms to convert (x, y) to (r, theta)
verts = [(r*cos(t) + x0, r*sin(t) + y0) for t in theta]
return Polygon(verts, closed=True)
def draw_circle_frame(self, x0, y0, r):
return Circle((x0, y0), r)
frame_dict = {'polygon': draw_poly_frame, 'circle': draw_circle_frame}
if frame not in frame_dict:
raise ValueError, 'unknown value for `frame`: %s' % frame
class RadarAxes(PolarAxes):
Class for creating a radar chart (a.k.a. a spider or star chart)
http://en.wikipedia.org/wiki/Radar_chart
name = 'radar'
# use 1 line segment to connect specified points
RESOLUTION = 1
# define draw_frame method
draw_frame = frame_dict[frame]
def fill(self, *args, **kwargs):
Override fill so that line is closed by default
closed = kwargs.pop('closed', True)
return super(RadarAxes, self).fill(closed=closed, *args, **kwargs)
def plot(self, *args, **kwargs):
Override plot so that line is closed by default
lines = super(RadarAxes, self).plot(*args, **kwargs)
for line in lines:
self._close_line(line)
def _close_line(self, line):
x, y = line.get_data()
# FIXME: markers at x[0], y[0] get doubled-up
if x[0] != x[-1]:
x = concatenate((x, [x[0]]))
y = concatenate((y, [y[0]]))
line.set_data(x, y)
def set_varlabels(self, labels):
self.set_thetagrids(theta * 180/pi, labels)
def get_axes_patch(self):
x0, y0 = (0.5, 0.5)
r = 0.5
return self.draw_frame(x0, y0, r)
register_projection(RadarAxes)
return theta
if __name__ == '__main__':
N = 5
theta = radar_factory(N)
# theta = radar_factory(N, frame='circle')
ax = subplot(111, projection='radar')
labels = ['humor', 'sarcasm', 'news content', 'America', 'overall']
colbert = [8, 9, 5, 9, 7]
dailyshow = [9, 6, 8, 3, 9]
# ax.plot(theta, dailyshow, 'b-o')
# ax.plot(theta, colbert, 'r-s')
ax.fill(theta, dailyshow, 'b')
ax.fill(theta, colbert, 'r')
for patch in ax.patches:
patch.set_alpha(0.5)
# FIXME: legend doesn't work when fill is called
# ax.legend(['The Daily Show', 'Colbert Report'])
ax.set_varlabels(labels)
# FIXME: rgrid lines don't appear; works if RESOLUTION is increased.
rgrids((2, 4, 6, 8, 10))
grid(True)
show()
-Tony
On Jun 20, 2008, at 12:16 AM, Curtis Jensen wrote:
No guarantees on when I'll have time, but I'll work on it.
Thanks for the info.
--
Curtis
On Thu, Jun 19, 2008 at 8:17 AM, John Hunter [EMAIL PROTECTED]
wrote:
On Wed, Jun 18, 2008 at 2:43 PM, Curtis Jensen [EMAIL PROTECTED]
wrote:
Nice. Thanks. I had tried to do something similar, but kept
getting
a curved line between each data point.
Also, I too got errors with a previous versions of matplotlib, but
0.98 works.
If someone were willing to add Radar plots to the matplotlib
functionality, would this be wanted by the users or maintainers?
Yes, certainly. You may want to take a look at the polar
implementation (can you inherit from it?) to reuse as much as
possible. Michael has also written a short guide to developers
working with nonlinear projections
http://matplotlib.sourceforge.net/doc/html/devel/add_new_projection.html
JDH
-
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Radar / Spider Chars
On Jun 15, 2008, at 11:54 AM, Curtis Jensen wrote: There was recently a post on Radar/Spider plotting (http://sourceforge.net/mailarchive/message.php?msg_id=4845303A.9050204%40epcc.ed.ac.uk ). I too am interested in creating Radar plots with matplot. Is there a simple way to do this? Here's a hack to get part of what you want: = from matplotlib.projections.polar import PolarAxes from pylab import * # Create 6 points (plus 7th point that matches the first) with coordinates r, theta N = 6 theta = 2 * pi * linspace(0, 1, N+1) r = rand(N+1) r[N] = r[0] # HACK: force PolarAxes to use 1 line segment to connect specified points PolarAxes.RESOLUTION = 1 ax = subplot(111, polar=True) c = ax.plot(theta, r, 'r-o') show() = I think this only works on matplotlib 0.98. I tried using rgrids and thetagrids to change the labels, but for some reason I was getting a TypeError when I called either of those functions. -Tony - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Easy question: how to select specific subplot for second (or more) time
Wow, a question I can actually answer: ax1 = subplot(211) ax2 = subplot(212) ax1.plot([1,2,3]) ax2.plot([4,3,2]) ax1.plot([3,2,1]) Best, -Tony On Jun 10, 2008, at 9:09 AM, Mark Bakker wrote: Hello list - I want to plot something in two subplots, then add something to the first subplot. How do I select the first subplot after I have plotted on the second subplot? For example: subplot(211) plot([1,2,3]) subplot(212) plot([4,3,2]) Now I want to add something to the first subplot. So I thought I could do subplot(211) again, but that destroys the subplot. Any suggestions? Thanks, Mark - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Easy question: how to select specific subplot for second (or more) time
Hey Mark, Actually, recalling subplot(211) seems to work for me. Strange. You may want to try forcing the first plot to remain before drawing the second: subplot(211) plot([1,2,3]) hold(True) subplot(212) plot([4,3,2]) subplot(211) plot([3,2,1]) -Tony On Jun 10, 2008, at 9:29 AM, Mark Bakker wrote: Thanks Tony - I was hoping there was a plyab-ish command. Like you can do Figure(1), Figure(2), and then reselect Figure(1) to get access to the first figure. No such command for subplot, I understand. Cheers, Mark On Tue, Jun 10, 2008 at 3:27 PM, Tony S Yu [EMAIL PROTECTED] wrote: Wow, a question I can actually answer: ax1 = subplot(211) ax2 = subplot(212) ax1.plot([1,2,3]) ax2.plot([4,3,2]) ax1.plot([3,2,1]) Best, -Tony On Jun 10, 2008, at 9:09 AM, Mark Bakker wrote: Hello list - I want to plot something in two subplots, then add something to the first subplot. How do I select the first subplot after I have plotted on the second subplot? For example: subplot(211) plot([1,2,3]) subplot(212) plot([4,3,2]) Now I want to add something to the first subplot. So I thought I could do subplot(211) again, but that destroys the subplot. Any suggestions? Thanks, Mark - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
