matplotlib-users Mailing List for matplotlib

Robert Kern wrote:
> George Nurser wrote:
> 
> 
>>It still seems to me a real 'gotcha' that if Z: doesn't work. Is there
>>any possibility of it being allowed to work in numpy?
> 
As Robert said, this was changed intentionally. The construct if Z: is 
usually used to determine if an argument was passed in. It is usually 
better to replace this construct with if Z is None: anyway.
The major problem is that the 'and' and the 'or' operations do "truth" 
value testing not "element-by-element" testing. This is going to cause 
an algorithmic error (but not raise an exception) over and over again. 
It is better to tell the person they are being ambiguous and move on.
I know it can be a bit of a pain to convert code that uses this 
construct, sorry about that. In the long run I think it will be better 
than having code that doesn't work because you forgot that 'and' and '&' 
 do two entirely different things.
-Travis

Darren,
I did a little more googling after my initial post and found that if 
I set:
font.latex.package : type1cm
text.usetex : true
text.tex.engine: latex
in my .matplotlibrc file the problem goes away. So I guess this is a 
false alarm, although I don't remember having problems with fonts in 
Latex in the past. Still, I think I've found my workaround. Thanks 
for your quick response, and apologies for not having done more 
research before posting.
Rick
On Feb 14, 2006, at 2:00 PM, Darren Dale wrote:
> Hi Rick,
>
>> Forgive me if this is a FAQ. I'm having trouble outputting fonts into
>> EPS files from matplotlib. If I plot a figure and then include the
>> figure in a LaTeX file, I get the figure minus the text in the xlabel
>> and ylabel fields. If I use Preview (I'm on a Mac) to show the
>> figure, the captions are there.
>>
>> Any idea what's wrong? Is there an easy workaround?
>
> I'm not sure. Maybe on of the Mac users can speak up, but in the 
> meantime,
> please make a barebones test script that will reproduce the 
> problem, run
> python test.py --verbose-debug, and post the output along with the 
> script
> and the resulting eps file. Also, please note any changes you have 
> made to
> your rc settings (for example, are you using the usetex option, 
> have you
> enabled ps.useafm, etc), and what version of mpl you are using.
>
>
Rick Muller
rm...@sa...

Hi Rick,
> Forgive me if this is a FAQ. I'm having trouble outputting fonts into
> EPS files from matplotlib. If I plot a figure and then include the
> figure in a LaTeX file, I get the figure minus the text in the xlabel
> and ylabel fields. If I use Preview (I'm on a Mac) to show the
> figure, the captions are there.
>
> Any idea what's wrong? Is there an easy workaround?
I'm not sure. Maybe on of the Mac users can speak up, but in the meantime,
please make a barebones test script that will reproduce the problem, run
python test.py --verbose-debug, and post the output along with the script
and the resulting eps file. Also, please note any changes you have made to
your rc settings (for example, are you using the usetex option, have you
enabled ps.useafm, etc), and what version of mpl you are using.

Forgive me if this is a FAQ. I'm having trouble outputting fonts into 
EPS files from matplotlib. If I plot a figure and then include the 
figure in a LaTeX file, I get the figure minus the text in the xlabel 
and ylabel fields. If I use Preview (I'm on a Mac) to show the 
figure, the captions are there.
Any idea what's wrong? Is there an easy workaround?
Thanks in advance,
Rick
Rick Muller
rm...@sa...

> But it does. The X and Y arrays give the coordinates of the Z points.
> If you want to reverse the Y axis, say to have Y increase downward, then
> you do something like this:
>
> a = gca()
> a.set_ylim(a.get_ylim()[::-1])
>
> There are many other ways to do it, but the point is that the axes are
> drawn with the first ylim value at the bottom and the second at the top,
> so to reverse the axis you simply reverse the order of the y limits.
> Similarly for the x-axis.
>
Fair enough, but notice that if I use imshow(Z, extent=[xmin, xmax,
ymax, min]), it displays the image with the ymax extent at the bottom and
ymin at the top of the y-axis, as I intended. For contour, the extent is
always displayed in increasing order in each axis.

Hanno,
See examples/image_masked.py. I think it does what you want. If your 
version of mpl is recent enough to include this demo, then you are all set.
Eric
Hanno Klemm wrote:
> Hi there,
> 
> is there a possibility to use imshow() with masked arrays? The
> problem: I have a large matrix where no_data_values are denominated by
> a certain number. It now would be very easy to mask these values and
> let imshow for example display them in another color but not use them
> in e.g. normalising the color scale. 
> 
> I think I saw some other mechansm to do that in the cookbook but I'm
> not sure if it can do what I want and at the moment the cookbook (or
> rather the scipy server) seems to be down.
> 
> Best regards,
> Hanno
> 
> 

Curtis,
Curtis Cooper wrote:
>>Now I see what you mean. The problem is that the extent kwarg works
>>only if the origin kwarg is also set and is not None. I have changed
>>the docstring accordingly. There was a reason I made that requirement,
>>but possibly it could be relaxed. The alternative is to simply generate
>>X and Y arrays that specify the coordinates of your Z points, and then
>>call contour(X, Y, Z, ...).
>>
> 
> 
> I think extent should work even if origin is not set, but at least if the
> documentation is clear about this, users can figure out the right thing to
> do easily enough.
OK, probably I will make the change (to allow use of extent without 
origin) soon, but I did not want to do it in too much of a hurry.
> 
> The alternative you mention does not allow plotting of the y-axis in
> reverse. For example, I often put pressure decreasing upward on the
> y-axis of my plots. It would be nice if contour(X, Y, Z, ...) respected
> my choice of ordering.
But it does. The X and Y arrays give the coordinates of the Z points. 
If you want to reverse the Y axis, say to have Y increase downward, then 
 you do something like this:
a = gca()
a.set_ylim(a.get_ylim()[::-1])
There are many other ways to do it, but the point is that the axes are 
drawn with the first ylim value at the bottom and the second at the top, 
 so to reverse the axis you simply reverse the order of the y limits. 
Similarly for the x-axis.
Eric

Ryan Krauss wrote:
> This is a common problem I have with switching code over to numpy. If
> you are in the habit of using if myMatrix: as a way to check for an
> empty matrix, numpy now throws this error. It could be replaced with
> myMatrix.any(), but then I think there are problems if you use the
> same code under Numeric or numarray.
sometrue() exists as a ufunc in both.
-- 
Robert Kern
rob...@gm...
"In the fields of hell where the grass grows high
 Are the graves of dreams allowed to die."
 -- Richard Harter

George Nurser wrote:
> It still seems to me a real 'gotcha' that if Z: doesn't work. Is there
> any possibility of it being allowed to work in numpy?
We've had a long discussion about this. No.
http://www.scipy.net/pipermail/scipy-dev/2005-November/thread.html#3799
In short, that "if Z:" worked in Numeric was a *huge* gotcha that got almost
everyone who ever used that feature.
-- 
Robert Kern
rob...@gm...
"In the fields of hell where the grass grows high
 Are the graves of dreams allowed to die."
 -- Richard Harter

On 14 Feb 2006, at 16:59, Ted Drain wrote:
> FYI: I believe the best way to check for None is to use:
>
> if Z is None
>
> or
>
> if Z is not None
>
> This eliminates the possibility of Z implementing the __cmp__ 
> method which would get called if you use "if Z == None". I only 
> know this after wasting several hours trying to figure out why some 
> code that looked perfectly reasonable wouldn't work after I
I've fallen into this trap too. Using if Z is None seems to be the 
*only* sensible way with numpy; it was explained in a mail of Robert 
Kern's last week.
It still seems to me a real 'gotcha' that if Z: doesn't work. Is 
there any possibility of it being allowed to work in numpy?
--George.

Dan Christensen <jd...@uw...> writes:
> I'd like to plot a large number of points (say 10**6 or 10**7) with
> different colours. The colours will not naturally be parametrized by
> a single float, but rather the rgb components will all vary
> independently, so I don't think I can use a colormap.
I ended up not using matplotlib for this, but for the sake of anyone
with a similar question, I'll briefly say what I did: I had my python
program write out raw postscript. This turned out to be extremely
efficient in both time and space, and allows very high-resolution
printouts from a relatively small postscript file. For example, one
plot with 13.5 million points is stored in an uncompressed postscript
file which is only 24MB, less than 2 bytes per point (and the points
vary in x, y coordinates, R,G,B colours and radii). I'm able to do
this by taking into account (non-linear) symmetries of the plot
(making the postscript code do some of the calculations) and by taking
into account patterns in the colours and radii.
I'd still love it if matplotlib's scatter command could handle small
round dots more efficiently, since I use it for most of my other work,
but for now the above is working for me.
Dan

FYI: I believe the best way to check for None is to use:
if Z is None
or
if Z is not None
This eliminates the possibility of Z implementing the __cmp__ method which 
would get called if you use "if Z == None". I only know this after wasting 
several hours trying to figure out why some code that looked perfectly 
reasonable wouldn't work after I adding a comparison method...
Ted
At 08:44 AM 2/14/2006, J.B...@if... wrote:
>Hello again,
>
>in mplot3d.py I changed line 729:
>
>- if Z:
>+if Z==None:
>
>Could this work too??? 'Python mplot3d.py' seems to work then but 'python
>surface.py' fails with:
>
>jens-ifw@x21lx-jensb:/media/exchange/Python/3d> python surface.py
>Traceback (most recent call last):
> File "surface.py", line 16, in ?
> ax = mplot3d.Axes3D(fig, axisbg='k')
>AttributeError: 'module' object has no attribute 'Axes3D'
>
>Cheers
>
>Jens
>
>
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Hello again,
in mplot3d.py I changed line 729:
- if Z:
+if Z==None:
Could this work too??? 'Python mplot3d.py' seems to work then but 'python
surface.py' fails with:
jens-ifw@x21lx-jensb:/media/exchange/Python/3d> python surface.py
Traceback (most recent call last):
 File "surface.py", line 16, in ?
 ax = mplot3d.Axes3D(fig, axisbg='k')
AttributeError: 'module' object has no attribute 'Axes3D'
Cheers
Jens

This is a common problem I have with switching code over to numpy. If
you are in the habit of using if myMatrix: as a way to check for an
empty matrix, numpy now throws this error. It could be replaced with
myMatrix.any(), but then I think there are problems if you use the
same code under Numeric or numarray.
Ryan
On 2/14/06, John Hunter <jdh...@ac...> wrote:
> >>>>> "J" =3D=3D J Brandenburg <J.B...@if...> writes:
>
> J> Hi Travis, Hi list,
>
> J> I saw Travis' query on the matplotlib-user - list and of cause
> J> I read Fernandos reply...
>
> J> So, I copied the three files into the matplotlib directory as
> J> bsp_3D01.py, proj3d.py and mplot3d.py... But if I try to run
> J> bsp_3d01.py I get:
>
> Not sure about the bsp example ...
>
> Try the following
>
> wget http://matplotlib.sourceforge.net/mpl3d.zip
> unzip mpl3d.zip
> cd 3d/
> python mplot3d.py --Numeric
>
> There is a problem with numpy support, since when I ran the code with
> numpy I got the following
>
> Traceback (most recent call last):
> File
> "/home/jdhunter/debs/matplotlib/usr/lib/python2.4/site-packages/matplot=
lib/backends/backend_gtk.py",
> line 303, in expose_event
> self._render_figure(self._pixmap, w, h)
> File
> "/home/jdhunter/debs/matplotlib/usr/lib/python2.4/site-packages/matplot=
lib/backends/backend_gtkagg.py",
> line 72, in _render_figure
> FigureCanvasAgg.draw(self)
> File
> "/usr/lib/python2.4/site-packages/matplotlib/backends/backend_agg.py",
> line 386, in draw
> self.figure.draw(renderer)
> File "/usr/lib/python2.4/site-packages/matplotlib/figure.py", line
> 528, in draw
> for a in self.axes: a.draw(renderer)
> File "mplot3d.py", line 714, in draw
> self.w_xaxis.draw(renderer)
> File "mplot3d.py", line 464, in draw
> tc =3D self.axes.tunit_cube(vals,renderer.M)
> File "mplot3d.py", line 680, in tunit_cube
> M =3D M or self.M
> ValueError: The truth value of an array with more than one element is
> ambiguous. Use a.any() or a.all()
>
>
>
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>>>>> "J" == J Brandenburg <J.B...@if...> writes:
 J> Hi Travis, Hi list,
 J> I saw Travis' query on the matplotlib-user - list and of cause
 J> I read Fernandos reply...
 J> So, I copied the three files into the matplotlib directory as
 J> bsp_3D01.py, proj3d.py and mplot3d.py... But if I try to run
 J> bsp_3d01.py I get:
Not sure about the bsp example ...
Try the following
 wget http://matplotlib.sourceforge.net/mpl3d.zip
 unzip mpl3d.zip
 cd 3d/
 python mplot3d.py --Numeric
There is a problem with numpy support, since when I ran the code with
numpy I got the following
Traceback (most recent call last):
 File
 "/home/jdhunter/debs/matplotlib/usr/lib/python2.4/site-packages/matplotlib/backends/backend_gtk.py",
 line 303, in expose_event
 self._render_figure(self._pixmap, w, h)
 File
 "/home/jdhunter/debs/matplotlib/usr/lib/python2.4/site-packages/matplotlib/backends/backend_gtkagg.py",
 line 72, in _render_figure
 FigureCanvasAgg.draw(self)
 File
 "/usr/lib/python2.4/site-packages/matplotlib/backends/backend_agg.py",
 line 386, in draw
 self.figure.draw(renderer)
 File "/usr/lib/python2.4/site-packages/matplotlib/figure.py", line
 528, in draw
 for a in self.axes: a.draw(renderer)
 File "mplot3d.py", line 714, in draw
 self.w_xaxis.draw(renderer)
 File "mplot3d.py", line 464, in draw
 tc = self.axes.tunit_cube(vals,renderer.M)
 File "mplot3d.py", line 680, in tunit_cube
 M = M or self.M
ValueError: The truth value of an array with more than one element is
 ambiguous. Use a.any() or a.all()

Hi Travis, Hi list,
I saw Travis' query on the matplotlib-user - list and of cause I read
Fernandos reply...
So, I copied the three files into the matplotlib directory as bsp_3D01.py,
proj3d.py and mplot3d.py... But if I try to run bsp_3d01.py I get:
jens-ifw@x21lx-jensb:/media/exchange/Python> python bsp_3D01.py
Traceback (most recent call last):
 File "bsp_3D01.py", line 32, in ?
 run1()
 File "bsp_3D01.py", line 20, in run1
 ax = mplot3d.Axes3D(fig)
AttributeError: 'module' object has no attribute 'Axes3D'
What do I have to do to get it running???
Thank's a lot
Jens Brandenburg

Hi there,
is there a possibility to use imshow() with masked arrays? The
problem: I have a large matrix where no_data_values are denominated by
a certain number. It now would be very easy to mask these values and
let imshow for example display them in another color but not use them
in e.g. normalising the color scale. 
I think I saw some other mechansm to do that in the cookbook but I'm
not sure if it can do what I want and at the moment the cookbook (or
rather the scipy server) seems to be down.
Best regards,
Hanno
-- 
Hanno Klemm
kl...@ph...

try pylab.show() after the line "pylab.plot..."
On 2/14/06, Titi Anggono <tia...@ya...> wrote:
>
> Hi all,
>
> I tried to use matplotlib to plot my data for the
> first time.
> Here is my script
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D
> import pylab
> fout=3Dpylab.load('..\mia.dat')
> t=3Dfout[:,0]
> x=3Dfout[:,1]
> y=3Dfout[:,2]
> z=3Dfout[:,3]
> pylab.plot(t,x)
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D
>
> I got nothing and got the following message:
> "[<matplotlib.lines.Line2D instance at 0x014362B0>]"
>
> Please tell me what wrong is with my script.
>
> Btw, when I typed fout, I got this
> "array (18147,4) , type =3D d, has 72588 elements".
> What is "d" ?
>
> Thanks
> Titi
>
>
> __________________________________________________
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>
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=3D121642
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> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Hi all,
I tried to use matplotlib to plot my data for the
first time.
Here is my script
===========================
import pylab
fout=pylab.load('..\mia.dat')
t=fout[:,0]
x=fout[:,1]
y=fout[:,2]
z=fout[:,3]
pylab.plot(t,x)
===========================
I got nothing and got the following message:
"[<matplotlib.lines.Line2D instance at 0x014362B0>]"
Please tell me what wrong is with my script.
Btw, when I typed fout, I got this
"array (18147,4) , type = d, has 72588 elements".
What is "d" ?
Thanks
Titi
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

> Now I see what you mean. The problem is that the extent kwarg works
> only if the origin kwarg is also set and is not None. I have changed
> the docstring accordingly. There was a reason I made that requirement,
> but possibly it could be relaxed. The alternative is to simply generate
> X and Y arrays that specify the coordinates of your Z points, and then
> call contour(X, Y, Z, ...).
>
I think extent should work even if origin is not set, but at least if the
documentation is clear about this, users can figure out the right thing to
do easily enough.
The alternative you mention does not allow plotting of the y-axis in
reverse. For example, I often put pressure decreasing upward on the
y-axis of my plots. It would be nice if contour(X, Y, Z, ...) respected
my choice of ordering.
Cheers,
Curtis

Curtis,
Now I see what you mean. The problem is that the extent kwarg works 
only if the origin kwarg is also set and is not None. I have changed 
the docstring accordingly. There was a reason I made that requirement, 
but possibly it could be relaxed. The alternative is to simply generate 
X and Y arrays that specify the coordinates of your Z points, and then 
call contour(X, Y, Z, ...).
Eric
Curtis Cooper wrote:
> Hi Eric,
> 
> I'm sorry; you are correct. I will examine your example more carefully.
> What doesn't seem to work is when I don't use imshow at all but just do
> contour(Z, extent=extent). That is, the axes are just rows and columns of
> the pixels, not the extent I specified, whereas the extent I specified
> shows up when I only use imshow.
> 
> Thanks,
> Curtis

Hi Eric,
I'm sorry; you are correct. I will examine your example more carefully.
What doesn't seem to work is when I don't use imshow at all but just do
contour(Z, extent=extent). That is, the axes are just rows and columns of
the pixels, not the extent I specified, whereas the extent I specified
shows up when I only use imshow.
Thanks,
Curtis
 * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Curtis S. Cooper, Graduate Research Assistant *
 * Lunar and Planetary Laboratory, University of Arizona *
 * http://www.lpl.arizona.edu/~curtis/		 *
 * Kuiper Space Sciences, Rm. 318 *
 * 1629 E. University Blvd., *
 * Tucson, AZ 85721 * * * * * * * * * * * * * * *
 * Wk: (520) 621-1471 *
 * * * * * * * * * * * *
On 2006年2月13日, Eric Firing wrote:
> Curtis Cooper wrote:
> > Eric,
> >
> > Craig is right, contour and contourf are ignoring the 'extent' kwarg. I
> > just tried the contour_image.py demo you referred to. I changed the value
> > of the image extent parameters, and they still do not show up.
> >
> > Cheers,
> > Curtis
>
> Curtis,
>
> What do you mean by "do not show up"? In contour_image.py, I changed
>
> extent = (-3,4,-4,3)
> to
> extent = (-30,40,-40,30)
>
> and the three subplots that use extent changed their x and y ranges by a
> factor of 10, as expected.
>
> Either there is a version problem or there is a misunderstanding, so you
> will need to be more specific. Please provide a minimal script that
> doesn't do what you think it should, and specify what it is that you
> think it should do.
>
> Thanks.
>
> Eric
>

Curtis Cooper wrote:
> Eric,
> 
> Craig is right, contour and contourf are ignoring the 'extent' kwarg. I
> just tried the contour_image.py demo you referred to. I changed the value
> of the image extent parameters, and they still do not show up.
> 
> Cheers,
> Curtis
Curtis,
What do you mean by "do not show up"? In contour_image.py, I changed
extent = (-3,4,-4,3)
to
extent = (-30,40,-40,30)
and the three subplots that use extent changed their x and y ranges by a 
factor of 10, as expected.
Either there is a version problem or there is a misunderstanding, so you 
will need to be more specific. Please provide a minimal script that 
doesn't do what you think it should, and specify what it is that you 
think it should do.
Thanks.
Eric

Eric,
Craig is right, contour and contourf are ignoring the 'extent' kwarg. I
just tried the contour_image.py demo you referred to. I changed the value
of the image extent parameters, and they still do not show up.
Cheers,
Curtis
 * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Curtis S. Cooper, Graduate Research Assistant *
 * Lunar and Planetary Laboratory, University of Arizona *
 * http://www.lpl.arizona.edu/~curtis/		 *
 * Kuiper Space Sciences, Rm. 318 *
 * 1629 E. University Blvd., *
 * Tucson, AZ 85721 * * * * * * * * * * * * * * *
 * Wk: (520) 621-1471 *
 * * * * * * * * * * * *

On Monday 13 February 2006 7:34 pm, Bill Baxter wrote:
> Sorry, I wasn't very clear. My thinking was like this:
> - matplotlib web pages don't mention support for numpy anywhere, just
> numeric and numarray
> - matplotlib web page says that the default is to use numeric
> - numpy is basically the successor to numeric plus numarray functionality
>
> - conclusion: if matplotlib actually does support numpy, and the web pages
> are just out of date, then probably numpy would now be the default instead
> of numeric, since it is the successor to numeric.
>
> But apparently there's a flaw in that thinking somewhere.
(This discussion should really be on the mpl list instead of numpy.)
numpy is not Numeric. matplotlib supports Numeric, numarray and numpy. Since 
numpy is currently stabilizing, and Numeric is already stable, I think it 
appropriate that Numeric is used unless numpy is asked for, at least until 
numpy-1.0 (not that its my decision).