matplotlib-users Mailing List for matplotlib

Hi mpl-users,
I have a web application in which I produce png files using
matplotlib. Unfortunately the files are quite big (up to ~300 kb). I
have however tried using the Linux tool pngnq to reduce the file size
with a factor ~3-4 with almost no degradation of the result. I
therefore wondered whether it is possible to setup matplotlib to do
something similar (from the source code the savefig method for png
files does not seem to use any keyword arguments). Here is the output
of the command pnginfo for the matplotlib output file and the pngnq
processed file:
0.0.0.0.0.0.20090517t00z.768.png...
 Image Width: 768 Image Length: 328
 Bitdepth (Bits/Sample): 8
 Channels (Samples/Pixel): 4
 Pixel depth (Pixel Depth): 32
 Colour Type (Photometric Interpretation): RGB with alpha channel
 Image filter: Single row per byte filter
 Interlacing: No interlacing
 Compression Scheme: Deflate method 8, 32k window
 Resolution: 5039, 5039 (pixels per meter)
 FillOrder: msb-to-lsb
 Byte Order: Network (Big Endian)
 Number of text strings: 0 of 0
 Offsets: 0, 0
0.0.0.0.0.0.20090517t00z.768-nq8.png...
 Image Width: 768 Image Length: 328
 Bitdepth (Bits/Sample): 8
 Channels (Samples/Pixel): 1
 Pixel depth (Pixel Depth): 8
 Colour Type (Photometric Interpretation): PALETTED COLOUR (256
colours, 0 transparent)
 Image filter: Single row per byte filter
 Interlacing: No interlacing
 Compression Scheme: Deflate method 8, 32k window
 Resolution: 0, 0 (unit unknown)
 FillOrder: msb-to-lsb
 Byte Order: Network (Big Endian)
 Number of text strings: 0 of 0
 Offsets: 0, 0
I am not using transparency for anything. For a web application a
reduction from 300 kb to 90 kb is really important so I hope you have
some good ideas. Otherwise I guess I will have to put in a call to
pngnq in my code (although I prefer to avoid calls to external
programs in the Python code when possible).
Best regards,
Jesper

On 5/17/2009 2:44 PM Jae-Joon Lee apparently wrote:
> I meant consistency with Matplotlib itself.
My point is that that is not well defined,
since most of the OO API in Matplotlib is
Python centric, but the subplot definition
is an exception.
So I am suggesting that any new functions
certainly should not propagate this anomaly.
 > I agree and I'm personally for python-centric interface throughout matplotlib.
 > I think what we need is to devise a new python-centric interface
 > (e.g., subplot2grid you suggested) and may try to deprecate subplot
 > eventually.
So, looking forward, keeping that anomaly isolated
will be important, so that changes do not need to
be made in additional locations. (Or so I claim...)
Cheers,
Alan Isaac

Hmm,
Is it working on your side from a bash shell as "ipython --pylab script
argument"
I couldn't make it work in this fashion. As I said whos list nothing :(
I am on Fedora 10 x86, Python 2.5.2, IPython 0.10.bzr.r1173
Without the pylab switch I see the interactive space with variables. I also
have plot imported from my script, however each time I have to call show()
to see the figure to be re-drawn.
To me, it seems one need to compromise: either to start ipython --pylab
first and call scripts using "run" magic command or like you suggested start
ipython with the script loaded and call show() after each plot command.
Please comment me if I am wrong...
Gökhan
On Sun, May 17, 2009 at 3:19 PM, Roy Hyunjin Han <
sta...@gm...> wrote:
> On Sun, May 17, 2009 at 2:17 PM, Gökhan SEVER <gok...@gm...>
> wrote:
> > Hello Roy,
> >
> > "ipython splot.py 09_03_23_11_44_54.stats.tas"
> >
> > works, but I can't make it work with pylab switch. It executes my script,
> > however whos list an empty namespace :(
>
> Gökhan,
>
> The "whos" command works for me.
>
> Also, why can't you use "import pylab" and make your plots directly in
> ipython?
> You can also use "from pylab import *" if you don't want to type pylab
> every time.
>
> In [1]: whos
> Variable Type Data/Info
> ----------------------------------------------------
> argv list ['splot.py',
> '09_03_23_11_44_54.stats.tas']
> argv_arr ndarray 12x13: 156 elems, type
> `float64`, 1248 bytes
> axes function <function axes at 0x92b6064>
> axis function <function axis at 0x92b6294>
> boxplot function <function boxplot at 0x92b6924>
> d09_03_23_11_44_54_stats_tas ndarray 12x13: 156 elems, type
> `float64`, 1248 bytes
> data_len int 12
> draw function <function draw at 0x9212dbc>
> f file <closed file
> '09_03_23_11<...>', mode 'r' at 0x88ef260>
> i int 11
> loadtxt function <function loadtxt at 0x8b65304>
> mouse_hover_formatx function <function
> mouse_hover_formatx at 0x88e84fc>
> mouse_hover_formaty function <function
> mouse_hover_formaty at 0x88e84c4>
> plot function <function plot at 0x92b6cdc>
> savefig function <function savefig at 0x9212df4>
> show function <function show at 0x920f72c>
> skiprows int 30
>

On Sun, May 17, 2009 at 2:17 PM, Gökhan SEVER <gok...@gm...> wrote:
> Hello Roy,
>
> "ipython splot.py 09_03_23_11_44_54.stats.tas"
>
> works, but I can't make it work with pylab switch. It executes my script,
> however whos list an empty namespace :(
Gökhan,
The "whos" command works for me.
Also, why can't you use "import pylab" and make your plots directly in ipython?
You can also use "from pylab import *" if you don't want to type pylab
every time.
In [1]: whos
Variable Type Data/Info
----------------------------------------------------
argv list ['splot.py',
'09_03_23_11_44_54.stats.tas']
argv_arr ndarray 12x13: 156 elems, type
`float64`, 1248 bytes
axes function <function axes at 0x92b6064>
axis function <function axis at 0x92b6294>
boxplot function <function boxplot at 0x92b6924>
d09_03_23_11_44_54_stats_tas ndarray 12x13: 156 elems, type
`float64`, 1248 bytes
data_len int 12
draw function <function draw at 0x9212dbc>
f file <closed file
'09_03_23_11<...>', mode 'r' at 0x88ef260>
i int 11
loadtxt function <function loadtxt at 0x8b65304>
mouse_hover_formatx function <function
mouse_hover_formatx at 0x88e84fc>
mouse_hover_formaty function <function
mouse_hover_formaty at 0x88e84c4>
plot function <function plot at 0x92b6cdc>
savefig function <function savefig at 0x9212df4>
show function <function show at 0x920f72c>
skiprows int 30

> Oops, sorry about that. Looks like I have it fixed now.
>
> JDH
>
Yes, it looks fine now.
Thanks!
-JJ

> Magnus Benjes wrote:
>> Hello,
>> in version 0.98.5.2 the polar plot still has a problem with negativ 
>> angles.
>> The polarplot is drawing a circle when the angle changes from negativ to 
>> positiv (e.g. from -0.01 to +0.01).
>
> Your example works fine with svn. I don't recall whether the problem was 
> fixed before the last release. I think it was.
>
Thank you for the hint, in version 0.98.6 the polar plot has no problems 
with negativ angles any more.
But now there are only gridlines in radial direction and the gridlines in 
angular direction are missing.
Magnus 

Hello Roy,
"ipython splot.py 09_03_23_11_44_54.stats.tas"
works, but I can't make it work with pylab switch. It executes my script,
however whos list an empty namespace :(
My aim of loading the variables and results into an interactive pylab
enabled workspace is to be able to continue working on the same data and if
necessary make some manipulations like adding titles, labels, legends,
changing scales depends on a person's need.
According to IPython documentation it is also possible to make IPython as
the default python environment. (
http://ipython.scipy.org/doc/nightly/html/interactive/reference.html#ipython-as-your-default-python-environment)
And again no way of starting with pylab ("there is no way to pass IPython
any command-line options")
Any other ideas?
Btw, I haven't seen a blue star lately :)
Gökhan
On Sun, May 17, 2009 at 7:07 AM, Roy Hyunjin Han <
sta...@gm...> wrote:
> On Sat, May 16, 2009 at 4:34 PM, Gökhan SEVER <gok...@gm...>
> wrote:
> >>> However I still couldn't figure out how to drop in ipython from the
> bash shell call
> >>> while all my variable context visible in the ipython namespace.
>
>
> Gökhan,
>
> Have you tried the following?
>
> RHH
>
>
> $ ipython splot.py 09_03_23_11_44_54.stats.tas
> Python 2.5.2 (r252:60911, Sep 30 2008, 15:41:38)
> Type "copyright", "credits" or "license" for more information.
>
> IPython 0.8.4 -- An enhanced Interactive Python.
> ? -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help -> Python's own help system.
> object? -> Details about 'object'. ?object also works, ?? prints more.
>
> In [1]: skiprows
> Out[1]: 30
>

Magnus Benjes wrote:
> Hello,
> in version 0.98.5.2 the polar plot still has a problem with negativ angles.
> The polarplot is drawing a circle when the angle changes from negativ to 
> positiv (e.g. from -0.01 to +0.01).
Your example works fine with svn. I don't recall whether the problem 
was fixed before the last release. I think it was.
> 
> But in "What new in 0.98.4" 
> (http://matplotlib.sourceforge.net/users/whats_new.html) I can read:
> "Fix polar interpolation to handle negative values of theta - MGD"
I think that commit actually introduced the problem.
> 
> Is there a workaround for this problem?
A release appears to be imminent--it was tagged hours ago. Can you 
update when it appears?
Eric
> 
> Regards
> Magnus
> 
> ********************
> import numpy as np
> import matplotlib
> import matplotlib.pyplot as plt
> 
> x = np.linspace(-np.pi/3, np.pi/3, 100)
> y = np.sin((10*x)**2)+2
> 
> plt.subplot(111, polar=True)
> plt.plot(x,y)
> plt.title(matplotlib.__version__)
> plt.show()
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
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On 5/17/2009 11:11 AM Linda_swe apparently wrote:
> ("total size of new array must be unchanged")
Again, this means what it says.
Your data array is the wrong size.
You cannot for example reshape a (3,) array into a (2,2) array.
http://www.scipy.org/Numpy_Example_List_With_Doc#head-11717acafb821da646a8db6997e59b820ac8761a
You can contour any 2d array.
You can optionally supply 1d coordinates.
http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.contourf
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> plt.contour(np.add.outer(np.arange(20),np.arange(20)))
<matplotlib.contour.ContourSet instance at 0x019BF4B8>
>>> plt.show()
Alan Isaac

Hi Alan,
Thanks and it works for y and x but i guess i dont know how to shapet Z
("total size of new array must be unchanged")
Overall i just dont get it how to calcuate the nlons and nlats fro Z.
yre = np.reshape(lats,nlats) 
xre = np.reshape(lons,nlons) 
print yre
print xre
zre = np.reshape(values,(nlats,nlons)).transpose() 
CT = plt.contourf(xre, yre, zre,58,cmap=plt.cm.jet)
cbar = plt.colorbar()
plt.show()
AlanIsaac wrote:
> 
> On 5/17/2009 10:21 AM Linda_swe apparently wrote:
>> atlest give me a hint...
> 
> The hint:
> 
>> error:list object has no attribute reshape
> 
> Listen to Python: all the info is there.
> A list is not a numpy array.
> Don't treat it like one.
> 
> However you can do:
> numpy.reshape(mylist, myshape)
> 
> Alan Isaac
> 
> ------------------------------------------------------------------------------
> 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
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
> 
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On 5/17/2009 10:21 AM Linda_swe apparently wrote:
> atlest give me a hint...
The hint:
> error:list object has no attribute reshape
Listen to Python: all the info is there.
A list is not a numpy array.
Don't treat it like one.
However you can do:
numpy.reshape(mylist, myshape)
Alan Isaac

Why dont anyone answer me???
atlest give me a hint...
Ok, so i want to use the my csv as input and then plot the contour. I have
the follwing code but gives
error:list object has no attribute reshape
is using list diffrent than using numpys loadtext and then into variables
???
from matplotlib.mlab import load
import matplotlib.pyplot as plt 
import numpy as np
import csv
portfolio = csv.reader(open("file.csv", "rb"))
portfolio_list = []
portfolio_list.extend(portfolio)
lats = []
lons = []
values=[]
for data in portfolio_list:
 lats.append(data[0])
 lons.append(data[1])
 values.append(data[2])
print lats
print lons
nlats = len(lats)
nlons = len(lons)
yre = lats.reshape(nlats,nlons)
xre = lons.reshape(nlats,nlons)
zre = values.reshape(nlats,nlons)
#### later in the defined map
CT = plt.contourf(xre, yre, zre, cmap=color_map)
cbar = plt.colorbar()
plt.show()
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On Sat, May 16, 2009 at 10:58 PM, Jae-Joon Lee <lee...@gm...> wrote:
>> http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#rgb-axes
>
> Thanks a lot, John.
> However, example figures are missing currently. (instead it shows a
> message "Exception occurred rendering plot.").
> Also, API documentations are not correctly generated also. My quick
> guess is that the axes_grid module was not found during the sphinx
> run. Can you take a look? The documentation builds fine for me.
Oops, sorry about that. Looks like I have it fixed now.
JDH

2009年5月17日 00:15:48 -0400, Jae-Joon Lee wrote:
> On Sat, May 16, 2009 at 6:58 PM, 
> <jor...@ya...> wrote:
>>
>> Hi,
>> I want to read images and do some processing with them. While learning
>> how to do this, i.e. opening images, displaying them, transforming them
>> tu numpy arrays, etc., I came across a strange behaviour. If I open an
>> image and use imshow() to display it, it comes upside down. See this
>> thread in the numpy mailing list for more details:
>> http://thread.gmane.org/gmane.comp.python.numeric.general/30148 .
>> Someone on that list suggested to check here if this behavior was
>> correct. Is it normal that the image appears upside down? If yes, can
>> someone explain what's going on?
> 
> Note that the image may be upside down for you but may be correct for
> others. The array itself does not know about the orientation of the
> image and you have to explicitly specify this.
I think the point here is that
	img = Image('foo.png')
	imshow(img)
and
	img = Image('foo.png')
	imshow(asarray(img))
give different results, since matplotlib.image.pil_to_array functions 
differently from what PIL exposes in __array_interface__
-- 
Pauli Virtanen

Hello,
in version 0.98.5.2 the polar plot still has a problem with negativ angles. 
The polarplot is drawing a circle when the angle changes from negativ to positiv (e.g. from -0.01 to +0.01).
But in "What new in 0.98.4" (http://matplotlib.sourceforge.net/users/whats_new.html) I can read:
"Fix polar interpolation to handle negative values of theta - MGD"
Is there a workaround for this problem?
Regards
Magnus
********************
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
x = np.linspace(-np.pi/3, np.pi/3, 100)
y = np.sin((10*x)**2)+2
plt.subplot(111, polar=True)
plt.plot(x,y)
plt.title(matplotlib.__version__)
plt.show()

On Sat, May 16, 2009 at 6:58 PM, <jor...@ya...> wrote:
>
> Hi,
> I want to read images and do some processing with them. While learning how to do this, i.e. opening images, displaying them, transforming them tu numpy arrays, etc., I came across a strange behaviour. If I open an image and use imshow() to display it, it comes upside down. See this thread in the numpy mailing list for more details: http://thread.gmane.org/gmane.comp.python.numeric.general/30148 . Someone on that list suggested to check here if this behavior was correct. Is it normal that the image appears upside down? If yes, can someone explain what's going on?
Note that the image may be upside down for you but may be correct for
others. The array itself does not know about the orientation of the
image and you have to explicitly specify this.
For imshow (and other similar commands), use the origin keyword. e.g.,
 >>> imshow(a, origin="lower")
http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.imshow
-JJ
>
> jorge
>
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Fri, May 15, 2009 at 10:02 PM, John Hunter <jd...@gm...> wrote:
> When you are extending/fixing existing code and come across methods
> with no docs, could you write a one or two line doc string for them?
> I wrote many of these and at the time they were so obvious that they
> didn't need docstrings, but as time passes and I reencounter them, I
> wish there was a simple line explaining them. As you are digging
> through the code figuring them all out, it is a great time to drop in
> a simple one-liner docstring (eg explaining what coord system is being
> returned by _get_position_xy). As the famous coding quip says, the
> literal wording or author of which I cannot dig up right now, "Leave
> comments in your code -- someone may read it someday, and that someone
> may be you!"
Sure, I'll keep that in mind.
I'll revise the patch (I'll also think about the contains method) and
submit it soon.
Thanks,
-JJ

On Fri, May 15, 2009 at 10:10 PM, John Hunter <jd...@gm...> wrote:
> FYI, several weeks ago I updated the official site-docs after you
> contributes the axes grid toolkit and docs:
>
> http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#rgb-axes
Thanks a lot, John.
However, example figures are missing currently. (instead it shows a
message "Exception occurred rendering plot.").
Also, API documentations are not correctly generated also. My quick
guess is that the axes_grid module was not found during the sphinx
run. Can you take a look? The documentation builds fine for me.
Regards,
-JJ