matplotlib-users Mailing List for matplotlib

On Mon, Feb 9, 2015 at 1:00 AM, Thomas Caswell <tca...@gm...> wrote:
> Sorry about the bad tarball, I forgot to clean my git directory before
> generating it. Another point in favor of using the gh tarball, I can't
> screw it up.
I switch to GH tarball, but I must say they are a lot different than
the SF ones (now we have 3 copies of the examples in doc/mpl_examples
lib/mpl_examples and examples) and contains quite a lot more files
(like the whole unit/ tree) and development files (.travis, .gitignore
and friends), but if that's a more reliable way to get new tarball,
I'm all for it - let's use this in the future :)
> This is the first I have seen that CVE.
>
> That PR is not included in 1.4.3 because it completely over-hauls how the
> Agg rendering works (and generated a whole bunch of other bugs along the
> way).
>
> Mike: Is there a way to fix up the security issues reported on just the
> 1.4.x branch with out pulling that whole patch back?
there is a patch[1] attached to the Debian bug[2], I'm about to apply
to the package and see how it goes, you might want to
investigate+apply it in the final release
[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?msg=5;filename=matplotlib-printf-buffer-overrun.patch;att=1;bug=775691
[2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=775691
Cheers,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi

Ryan,
Thanks again. I have the permissions, I'll reinstall.
John
On 2/12/2015 11:43 AM, Ryan Nelson wrote:
> John,
>
> It's been a little while since I installed QGIS on my machine, but I 
> wonder if you missed a selection somewhere in the installation 
> process. Can you reinstall QGIS? (i.e. do you have admin permissions?) 
> There might be a number of selections you can make when installing, 
> and my guess is that you missed a selection to have the proper Python 
> libraries installed. Maybe there is a "Full" installation option, 
> which puts everything on your machine. As I said on my installation of 
> QGIS, that code works just fine, and I'm certain that I haven't done 
> anything special post-install.
>
> Ryan
>
> On Thu, Feb 12, 2015 at 12:37 PM, john polo <jp...@ma... 
> <mailto:jp...@ma...>> wrote:
>
> Ryan,
> I used the first line of your example and this was the result:
> Traceback (most recent call last):
> File "<input>", line 1, in <module>
> File "C:/OSGEO4~1/apps/qgis/./python\qgis\utils.py", line 454,
> in _import
> mod = _builtin_import(name, globals, locals, fromlist, level)
> ImportError: No module named matplotlib.pyplot
>
> I'm not sure what the first command is to confirm whether a module
> is installed or not, but it looks like I may need that.
> Thanks, Ben and Ryan.
>
> John
>
>
> On 2/12/2015 10:09 AM, Ryan Nelson wrote:
>> John,
>>
>> As Ben said, the QGIS Windows installer comes with its own Python
>> installation, which doesn't know anything about any other Python
>> install. Unfortunately, this apparently makes it rather difficult
>> to install other packages. However, QGIS Python already contains
>> Numpy and Matplotlib and PyQt4, which is what you need here. From
>> the Plugins dropdown menu, select Python Console. In the console
>> that opens at the bottom of the screen, you should be able to
>> type (don't type the > characters):
>> >>> import matplotlib.pyplot as plt
>> >>> plt.plot([1,2,3])
>> >>> plt.show()
>>
>> On my install of QGIS, that opens a pop-up window with a plot of
>> those data points. Does this throw an error for you too?
>>
>> Ryan
>>
>> On Thu, Feb 12, 2015 at 10:35 AM, john polo <jp...@ma...
>> <mailto:jp...@ma...>> wrote:
>>
>> Users,
>> I am working on Windows 7 with QGIS 2.4. I am trying to get a
>> plugin
>> installed in QGIS called Semi-Automatic Classification Plugin
>> to work.
>> The plugin is demonstrated here:
>> http://fromgistors.blogspot.com/2013/07/working-with-multispectral-bands-in-qgis.html
>>
>> The first time I tried to install the QGIS plugin, I got an error
>> message that backend_qt4agg was not installed. I installed
>> Python(x,y)
>> with Python 2.x, because it seemed like the easiest way to get
>> matplotlib and a bunch of other apps/extensions installed at
>> the same
>> time with minimal effort. I am not a programmer and I'm not
>> familiar
>> with installing things from source and then configuring
>> settings. After
>> the Python(x,y) install, I went to QGIS and started again and
>> tried to
>> install the plugin. I got the same error message. Please tell
>> me what I
>> need to do to get this backend installed in order to get the
>> QGIS plugin
>> I want.
>>
>> John Polo
>>
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming. The Go Parallel
>> Website,
>> sponsored by Intel and developed in partnership with Slashdot
>> Media, is your
>> hub for all things parallel software development, from weekly
>> thought
>> leadership blogs to news, videos, case studies, tutorials and
>> more. Take a
>> look and join the conversation now.
>> http://goparallel.sourceforge.net/
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> <mailto:Mat...@li...>
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
>

John,
It's been a little while since I installed QGIS on my machine, but I wonder
if you missed a selection somewhere in the installation process. Can you
reinstall QGIS? (i.e. do you have admin permissions?) There might be a
number of selections you can make when installing, and my guess is that you
missed a selection to have the proper Python libraries installed. Maybe
there is a "Full" installation option, which puts everything on your
machine. As I said on my installation of QGIS, that code works just fine,
and I'm certain that I haven't done anything special post-install.
Ryan
On Thu, Feb 12, 2015 at 12:37 PM, john polo <jp...@ma...> wrote:
> Ryan,
> I used the first line of your example and this was the result:
> Traceback (most recent call last):
> File "<input>", line 1, in <module>
> File "C:/OSGEO4~1/apps/qgis/./python\qgis\utils.py", line 454, in _import
> mod = _builtin_import(name, globals, locals, fromlist, level)
> ImportError: No module named matplotlib.pyplot
>
> I'm not sure what the first command is to confirm whether a module is
> installed or not, but it looks like I may need that.
> Thanks, Ben and Ryan.
>
> John
>
>
> On 2/12/2015 10:09 AM, Ryan Nelson wrote:
>
> John,
>
> As Ben said, the QGIS Windows installer comes with its own Python
> installation, which doesn't know anything about any other Python install.
> Unfortunately, this apparently makes it rather difficult to install other
> packages. However, QGIS Python already contains Numpy and Matplotlib and
> PyQt4, which is what you need here. From the Plugins dropdown menu, select
> Python Console. In the console that opens at the bottom of the screen, you
> should be able to type (don't type the > characters):
> >>> import matplotlib.pyplot as plt
> >>> plt.plot([1,2,3])
> >>> plt.show()
>
> On my install of QGIS, that opens a pop-up window with a plot of those
> data points. Does this throw an error for you too?
>
> Ryan
>
> On Thu, Feb 12, 2015 at 10:35 AM, john polo <jp...@ma...> wrote:
>
>> Users,
>> I am working on Windows 7 with QGIS 2.4. I am trying to get a plugin
>> installed in QGIS called Semi-Automatic Classification Plugin to work.
>> The plugin is demonstrated here:
>>
>> http://fromgistors.blogspot.com/2013/07/working-with-multispectral-bands-in-qgis.html
>>
>> The first time I tried to install the QGIS plugin, I got an error
>> message that backend_qt4agg was not installed. I installed Python(x,y)
>> with Python 2.x, because it seemed like the easiest way to get
>> matplotlib and a bunch of other apps/extensions installed at the same
>> time with minimal effort. I am not a programmer and I'm not familiar
>> with installing things from source and then configuring settings. After
>> the Python(x,y) install, I went to QGIS and started again and tried to
>> install the plugin. I got the same error message. Please tell me what I
>> need to do to get this backend installed in order to get the QGIS plugin
>> I want.
>>
>> John Polo
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming. The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is
>> your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
>> look and join the conversation now. http://goparallel.sourceforge.net/
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>
>

Ryan,
I used the first line of your example and this was the result:
Traceback (most recent call last):
 File "<input>", line 1, in <module>
 File "C:/OSGEO4~1/apps/qgis/./python\qgis\utils.py", line 454, in _import
 mod = _builtin_import(name, globals, locals, fromlist, level)
ImportError: No module named matplotlib.pyplot
I'm not sure what the first command is to confirm whether a module is 
installed or not, but it looks like I may need that.
Thanks, Ben and Ryan.
John
On 2/12/2015 10:09 AM, Ryan Nelson wrote:
> John,
>
> As Ben said, the QGIS Windows installer comes with its own Python 
> installation, which doesn't know anything about any other Python 
> install. Unfortunately, this apparently makes it rather difficult to 
> install other packages. However, QGIS Python already contains Numpy 
> and Matplotlib and PyQt4, which is what you need here. From the 
> Plugins dropdown menu, select Python Console. In the console that 
> opens at the bottom of the screen, you should be able to type (don't 
> type the > characters):
> >>> import matplotlib.pyplot as plt
> >>> plt.plot([1,2,3])
> >>> plt.show()
>
> On my install of QGIS, that opens a pop-up window with a plot of those 
> data points. Does this throw an error for you too?
>
> Ryan
>
> On Thu, Feb 12, 2015 at 10:35 AM, john polo <jp...@ma... 
> <mailto:jp...@ma...>> wrote:
>
> Users,
> I am working on Windows 7 with QGIS 2.4. I am trying to get a plugin
> installed in QGIS called Semi-Automatic Classification Plugin to work.
> The plugin is demonstrated here:
> http://fromgistors.blogspot.com/2013/07/working-with-multispectral-bands-in-qgis.html
>
> The first time I tried to install the QGIS plugin, I got an error
> message that backend_qt4agg was not installed. I installed Python(x,y)
> with Python 2.x, because it seemed like the easiest way to get
> matplotlib and a bunch of other apps/extensions installed at the same
> time with minimal effort. I am not a programmer and I'm not familiar
> with installing things from source and then configuring settings.
> After
> the Python(x,y) install, I went to QGIS and started again and tried to
> install the plugin. I got the same error message. Please tell me
> what I
> need to do to get this backend installed in order to get the QGIS
> plugin
> I want.
>
> John Polo
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot
> Media, is your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and
> more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> <mailto:Mat...@li...>
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Definitely. Assuming you don't want to do this in an interactive manner
(i.e. pointing and clicking with your mouse:
fig, ax = plt.subplots()
ax.contour(...)
ax.plot(x_dots, y_dots, 'ro', label='Dots')
-p
On Thu, Feb 12, 2015 at 8:07 AM, Dr Sydney Shall <syd...@me...>
wrote:
> I am a beginner and I use Python 2.7 on an iMac OSX 10.9.5. Python is
> the Enthought installation.
> I am doing simulation experiments. I have constructed a 2D contour map
> with my results and I am happy with the result.
> I am wondering if it is possible to add the data points, say as red
> dots, on this contour map.
> I have not been able to find an equivalent example in gallery and I am
> too much a novice to know what to do.
> Any help would be much appreciated.
>
> --
> Sydney
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

I am a beginner and I use Python 2.7 on an iMac OSX 10.9.5. Python is 
the Enthought installation.
I am doing simulation experiments. I have constructed a 2D contour map 
with my results and I am happy with the result.
I am wondering if it is possible to add the data points, say as red 
dots, on this contour map.
I have not been able to find an equivalent example in gallery and I am 
too much a novice to know what to do.
Any help would be much appreciated.
-- 
Sydney

John,
As Ben said, the QGIS Windows installer comes with its own Python
installation, which doesn't know anything about any other Python install.
Unfortunately, this apparently makes it rather difficult to install other
packages. However, QGIS Python already contains Numpy and Matplotlib and
PyQt4, which is what you need here. From the Plugins dropdown menu, select
Python Console. In the console that opens at the bottom of the screen, you
should be able to type (don't type the > characters):
>>> import matplotlib.pyplot as plt
>>> plt.plot([1,2,3])
>>> plt.show()
On my install of QGIS, that opens a pop-up window with a plot of those data
points. Does this throw an error for you too?
Ryan
On Thu, Feb 12, 2015 at 10:35 AM, john polo <jp...@ma...> wrote:
> Users,
> I am working on Windows 7 with QGIS 2.4. I am trying to get a plugin
> installed in QGIS called Semi-Automatic Classification Plugin to work.
> The plugin is demonstrated here:
>
> http://fromgistors.blogspot.com/2013/07/working-with-multispectral-bands-in-qgis.html
>
> The first time I tried to install the QGIS plugin, I got an error
> message that backend_qt4agg was not installed. I installed Python(x,y)
> with Python 2.x, because it seemed like the easiest way to get
> matplotlib and a bunch of other apps/extensions installed at the same
> time with minimal effort. I am not a programmer and I'm not familiar
> with installing things from source and then configuring settings. After
> the Python(x,y) install, I went to QGIS and started again and tried to
> install the plugin. I got the same error message. Please tell me what I
> need to do to get this backend installed in order to get the QGIS plugin
> I want.
>
> John Polo
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

I doubt that installing Python(x,y) would help because it is a
self-contained distribution of python. QGIS wouldn't necessarally know
about the libraries that it provides. Your best bet is to ask this question
to the QGIS people who better understands how their software is installed
in the Windows environment. How QGIS is installed is critical to
understanding what libraries it can and can not access.
Of course, you could also try one of the windows binary installers of
matplotlib, but I don't know if they come with the Qt4 environment or not.
Cheers!
Ben Root
On Thu, Feb 12, 2015 at 10:35 AM, john polo <jp...@ma...> wrote:
> Users,
> I am working on Windows 7 with QGIS 2.4. I am trying to get a plugin
> installed in QGIS called Semi-Automatic Classification Plugin to work.
> The plugin is demonstrated here:
>
> http://fromgistors.blogspot.com/2013/07/working-with-multispectral-bands-in-qgis.html
>
> The first time I tried to install the QGIS plugin, I got an error
> message that backend_qt4agg was not installed. I installed Python(x,y)
> with Python 2.x, because it seemed like the easiest way to get
> matplotlib and a bunch of other apps/extensions installed at the same
> time with minimal effort. I am not a programmer and I'm not familiar
> with installing things from source and then configuring settings. After
> the Python(x,y) install, I went to QGIS and started again and tried to
> install the plugin. I got the same error message. Please tell me what I
> need to do to get this backend installed in order to get the QGIS plugin
> I want.
>
> John Polo
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Users,
I am working on Windows 7 with QGIS 2.4. I am trying to get a plugin 
installed in QGIS called Semi-Automatic Classification Plugin to work. 
The plugin is demonstrated here:
http://fromgistors.blogspot.com/2013/07/working-with-multispectral-bands-in-qgis.html
The first time I tried to install the QGIS plugin, I got an error 
message that backend_qt4agg was not installed. I installed Python(x,y) 
with Python 2.x, because it seemed like the easiest way to get 
matplotlib and a bunch of other apps/extensions installed at the same 
time with minimal effort. I am not a programmer and I'm not familiar 
with installing things from source and then configuring settings. After 
the Python(x,y) install, I went to QGIS and started again and tried to 
install the plugin. I got the same error message. Please tell me what I 
need to do to get this backend installed in order to get the QGIS plugin 
I want.
John Polo

Thanks Paul, your explanation makes perfectly sense.
Indeed, computing "manually" the PDS (using numpy.fft) in a test case gives
me equal power for sine wave component of same amplitude, even when a
component is in the highest frequency bin.
However, giving the same test case to matplotlib.mlab.specgram() results in
the power density of the highest frequency bin being higher than the other
components.
For the test see this notebook:
http://nbviewer.ipython.org/gist/tritemio/162925a69a6ec29cdfe1
Antonio
On Wed, Feb 11, 2015 at 8:50 PM, Paul Blelloch <pau...@at...>
wrote:
> I’m just answering off the top of my head, but it would seem to make sense
> to me that neither the 0 frequency nor the fmax frequency should be scaled
> by 2. If you take an FFT of a signal of length N, you’ll get a transform
> of length N. N/2 points will correspond to positive frequencies, one point
> to zero frequency and N/2-1 points to negative frequency. So it’s the
> N/2-1 points that are reflected to the positive frequency axis, and the
> fmax frequency is the only one that doesn’t have a corresponding point on
> the negative axis.
>
>
>
> On the practical side, I’d say that you’re asking for trouble if you’re
> looking at the last frequency bin in a power spectrum. If there’s any
> significant energy in that bin, there’s almost certainly energy at higher
> frequencies that’s being aliased down. You really need to make sure that
> you have negligible power content before you get to the Nyquist frequency,
> usually by applying an analog filter to the data, or otherwise knowing that
> it cannot have undesired high frequency content.
>
>
>
> *From:* Antonino Ingargiola [mailto:tri...@gm...]
> *Sent:* Wednesday, February 11, 2015 6:45 PM
> *To:* mat...@li...
> *Subject:* [Matplotlib-users] mlab: computing power spectra
>
>
>
> Hi to all,
>
>
>
> I'm computing some spectrograms using the convenient functions defined in
> matplotlib.mlab.
>
>
>
> I found something that I don't completely understand. In computing the PSD
> the onesided power spectrum is scaled by a factor of 2 except for the first
> and the last bin:
>
>
>
>
> https://github.com/matplotlib/matplotlib/blob/v1.4.2/lib/matplotlib/mlab.py#L776
>
>
>
> in principle this should account for the contributions that in a two-sided
> spectrum is spread over negative and positive frequencies. However the lack
> of scaling in the highest frequency seems to cause a systematic
> underestimation on that frequency bin.
>
>
>
> Is it possible that the power spectrum should be scaled, in the case of
> even-length signal, up to the last bin (so that -1 in the slicing should be
> removed)?
>
>
>
> With correct scaling a signal comprised of two sinusoids of same power,
> one being at the Nyquist frequency, should have the same amplitude
> (excluding scallopping losses). I don't have time to test it at the moment,
> but maybe someone more expert can already tell me if I'm missing something
> or the matplotlib scaling is wrong.
>
>
>
> Thanks,
>
> Antonio
>

Hi to all,
I'm computing some spectrograms using the convenient functions defined in
matplotlib.mlab.
I found something that I don't completely understand. In computing the PSD
the onesided power spectrum is scaled by a factor of 2 except for the first
and the last bin:
https://github.com/matplotlib/matplotlib/blob/v1.4.2/lib/matplotlib/mlab.py#L776
in principle this should account for the contributions that in a two-sided
spectrum is spread over negative and positive frequencies. However the lack
of scaling in the highest frequency seems to cause a systematic
underestimation on that frequency bin.
Is it possible that the power spectrum should be scaled, in the case of
even-length signal, up to the last bin (so that -1 in the slicing should be
removed)?
With correct scaling a signal comprised of two sinusoids of same power, one
being at the Nyquist frequency, should have the same amplitude (excluding
scallopping losses). I don't have time to test it at the moment, but maybe
someone more expert can already tell me if I'm missing something or the
matplotlib scaling is wrong.
Thanks,
Antonio