matplotlib-users — Discussion related to using matplotlib

Re: [Matplotlib-users] numpoints in legend() function for scatter plot is not working in matplotlib 1.1.0?

[Chao Y. <cha...@gm...>]

Hi Ben,

I think I installed this version by following the instructions on
matplotlib website. But when I try to use git log, I get:

chaoyue@chaoyue-Aspire-4750:/usr/local/lib/python2.7/dist-packages/matplotlib$
pwd
/usr/local/lib/python2.7/dist-packages/matplotlib

chaoyue@chaoyue-Aspire-4750:/usr/local/lib/python2.7/dist-packages/matplotlib$
git log
fatal: Not a git repository (or any of the parent directories): .git

I tried to have a look at __init__.py, it has:

from __future__ import print_function

__version__  = '1.2.x'
__version__numpy__ = '1.4' # minimum required numpy version

So it's the correct directory I am going. could you give some further
instructions?

Chao

On Mon, Sep 10, 2012 at 3:05 PM, Benjamin Root <ben...@ou...> wrote:

>
>
> On Mon, Sep 10, 2012 at 2:56 AM, Chao YUE <cha...@gm...> wrote:
>
>> Hi Ben,
>>
>> I tried the "numpoints" in legend function for scatter plot, in dev
>> version and GTKAgg backend it works.
>>
>> In [3]: mat.__version__
>> Out[3]: '1.2.x'
>>
>> In [4]: mat.get_backend()
>> Out[4]: 'GTKAgg'
>>
>> Chao
>>
>>
> Strange, when I tested it last night, I was using a build of mpl from
> master of a couple weeks ago, and I saw three markers in the legend.  Now,
> I am trying it again with the latest master:
> 1478a1be70b3077b71350cecaccb774f76a76656, and I now see *zero* markers.
> Something is seriously broken.
>
> Can you tell me what commit (and the date for that commit) shows up at top
> when you run "git log" in the mpl source directory?
>
> Ben Root
>
>


-- 
***********************************************************************************
Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
************************************************************************************

Re: [Matplotlib-users] numpoints in legend() function for scatter plot is not working in matplotlib 1.1.0?

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

On Mon, Sep 10, 2012 at 2:56 AM, Chao YUE <cha...@gm...> wrote:

> Hi Ben,
>
> I tried the "numpoints" in legend function for scatter plot, in dev
> version and GTKAgg backend it works.
>
> In [3]: mat.__version__
> Out[3]: '1.2.x'
>
> In [4]: mat.get_backend()
> Out[4]: 'GTKAgg'
>
> Chao
>
>
Strange, when I tested it last night, I was using a build of mpl from
master of a couple weeks ago, and I saw three markers in the legend.  Now,
I am trying it again with the latest master:
1478a1be70b3077b71350cecaccb774f76a76656, and I now see *zero* markers.
Something is seriously broken.

Can you tell me what commit (and the date for that commit) shows up at top
when you run "git log" in the mpl source directory?

Ben Root

Re: [Matplotlib-users] markeredgecolor (mec) in the plot function not working?

[Chao Y. <cha...@gm...>]

Dear Ben,

I tried again with dev version and GTKAgg backend it works.

In [3]: mat.__version__
Out[3]: '1.2.x'

In [4]: mat.get_backend()
Out[4]: 'GTKAgg'

Chao


On Sun, Sep 9, 2012 at 9:32 PM, Benjamin Root <ben...@ou...> wrote:

>
>
> On Tue, Apr 10, 2012 at 12:22 PM, wiswit <cha...@gm...> wrote:
>
>> Dear all, I use matplotlib 1.1.0. import matplotlib.pyplot as plt
>> plt.plot(np.arange(10),'ro',mec='none') when I use plt.show(), there is
>> only blank frame with axis not no points. but plt.plot(np.arange(10),'ro')
>> will give good plot with read filled circles and black edges.
>> plt.scatter(np.arange(10),np.arange(10),c='r',marker='o',edgecolor='none')
>> is working fine. but I really think plt.plot is a very good and easy
>> function if you don't make complex scatter points. and the circles look
>> much nicer than that produced by plt.scatter (thought I don't know why as
>> they use the same symble....) does anyone else have found the same ? thanks
>> to all, Chao
>>
>
>
> This works for me with GTKAgg backend.  If this is still a problem for
> you, which backend are you using?
>
> Ben Root
>



-- 
***********************************************************************************
Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
************************************************************************************

Re: [Matplotlib-users] numpoints in legend() function for scatter plot is not working in matplotlib 1.1.0?

[Chao Y. <cha...@gm...>]

Hi Ben,

I tried the "numpoints" in legend function for scatter plot, in dev version
and GTKAgg backend it works.

In [3]: mat.__version__
Out[3]: '1.2.x'

In [4]: mat.get_backend()
Out[4]: 'GTKAgg'

Chao


On Sun, Sep 9, 2012 at 9:28 PM, Benjamin Root <ben...@ou...> wrote:

>
>
> On Tue, Apr 10, 2012 at 12:43 PM, wiswit <cha...@gm...> wrote:
>
>>
>> Dear all,
>>
>> I found that the numpoints in legend function for scatter plot is not
>> working?
>>
>> import matplotlib as mat
>> import matplotlib.pyplot as plt
>> In [59]: mat.__version__
>> Out[59]: '1.1.0'
>>
>> #ordinary plot working
>> fig=plt.figure()
>> ax=fig.add_subplot(111)
>> ax.plot(np.arange(10),'ro',label='tst')
>> ax.legend(numpoints=1)
>> plt.show()
>>
>> #but not scatter plot
>> fig=plt.figure()
>> ax=fig.add_subplot(111)
>> ax.scatter(np.arange(10),np.arange(10),marker='o',label='tst')
>> ax.legend(numpoints=1)
>> plt.show()
>>
>> cheers,
>>
>> chao
>>
>>
> Confirmed... this is still broken.
>
> Ben Root
>



-- 
***********************************************************************************
Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
************************************************************************************

[Matplotlib-users] ANN: mplstereonet v0.2 - Stereonets for matplotlib

[Joe K. <jof...@gm...>]

Announcement - mplstereonet v0.2
=========================

mplstereonet provides lower-hemisphere equal-area and equal-angle
stereonets for matplotlib.

Download
--------------

Available for download at: http://pypi.python.org/pypi/mplstereonet/0.2

See the github page for more information and development versions:
https://github.com/joferkington/mplstereonet

About
---------

Stereonets are a type of plot commonly used in the geosciences for
visualizing and analyzing orientation data.

Orientations of linear and planar features are plotted as the intersection
of the feature with a hemisphere.  (Therefore, linear features plot as
points and planar features plot as lines.)

mplstereonet provides plotting of planes (measured as strikes and dips),
poles to planes, and lineations (measured as rakes along a plane or as
plunges and bearings).

Additionally, mplstereonet provides orientation density contouring using a
variety of standard methods (e.g. "Kamb" contouring, etc).

Getting Started
----------------------

The easiest way to get started is to have a look at the examples:
https://github.com/joferkington/mplstereonet/tree/master/examples

Additionally, the readme has an overview and various examples:
https://github.com/joferkington/mplstereonet/blob/master/README.rst

Changes
-------------

New features in version 0.2 include:

- Density contouring of orientation data using a variety of methods
- Equal-angle as well as equal-area stereonets
- A variety of parsing utilities
- Geometric analysis utilities (e.g. plane intersections)

Thank you all very much!
-Joe Kington

Re: [Matplotlib-users] markeredgecolor (mec) in the plot function not working?

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

On Tue, Apr 10, 2012 at 12:22 PM, wiswit <cha...@gm...> wrote:

> Dear all, I use matplotlib 1.1.0. import matplotlib.pyplot as plt
> plt.plot(np.arange(10),'ro',mec='none') when I use plt.show(), there is
> only blank frame with axis not no points. but plt.plot(np.arange(10),'ro')
> will give good plot with read filled circles and black edges.
> plt.scatter(np.arange(10),np.arange(10),c='r',marker='o',edgecolor='none')
> is working fine. but I really think plt.plot is a very good and easy
> function if you don't make complex scatter points. and the circles look
> much nicer than that produced by plt.scatter (thought I don't know why as
> they use the same symble....) does anyone else have found the same ? thanks
> to all, Chao
>


This works for me with GTKAgg backend.  If this is still a problem for you,
which backend are you using?

Ben Root

Re: [Matplotlib-users] numpoints in legend() function for scatter plot is not working in matplotlib 1.1.0?

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

On Tue, Apr 10, 2012 at 12:43 PM, wiswit <cha...@gm...> wrote:

>
> Dear all,
>
> I found that the numpoints in legend function for scatter plot is not
> working?
>
> import matplotlib as mat
> import matplotlib.pyplot as plt
> In [59]: mat.__version__
> Out[59]: '1.1.0'
>
> #ordinary plot working
> fig=plt.figure()
> ax=fig.add_subplot(111)
> ax.plot(np.arange(10),'ro',label='tst')
> ax.legend(numpoints=1)
> plt.show()
>
> #but not scatter plot
> fig=plt.figure()
> ax=fig.add_subplot(111)
> ax.scatter(np.arange(10),np.arange(10),marker='o',label='tst')
> ax.legend(numpoints=1)
> plt.show()
>
> cheers,
>
> chao
>
>
Confirmed... this is still broken.

Ben Root

Re: [Matplotlib-users] plt.close() not releasing memory? Or memory leak elsewhere?

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

On Tue, May 22, 2012 at 9:18 AM, Stevenson, Samuel <
Sam...@co...> wrote:

> Hi Ben****
>
> ** **
>
> I am using 1.0.0. My colleague has 1.1.0 installed on his machine and is
> able to reproduce the same problem.****
>
> ** **
>
> Thanks****
>
>
> Sam
>

Going through my old unresolved emails, I came across this one.  I suspect
that whatever has caused this problem in v1.1.0 is still present in v1.2.0
that we will be putting out an RC for.  If you can make a small script that
can demonstrate the memory leak, maybe we can track it down and nail this
sucker before the final release?

Cheers!
Ben Root

Re: [Matplotlib-users] Saving figure instance for reuse

[Eric F. <ef...@ha...>]

On 2012/09/09 8:50 AM, Benjamin Root wrote:
>
>
> On Wed, Aug 15, 2012 at 5:40 AM, Jesper Larsen <jes...@gm...
> <mailto:jes...@gm...>> wrote:
>
>     Hi Matplotlib users
>
>     I have an application where performance is critical and matplotlib is
>     the performance bottleneck. I am making a lot of figures using the
>     same basic setup of the figure. And from my profiling I can see that
>     this basic setup accounts for most of the CPU time. Let us say that I
>     make a given figure including some axes. My questions are:
>
>     1. Can I make a copy of this figure including axes (copy.deepcopy does
>     not work on Figure objects) and use the copy for plotting on?
>
>     2. And how? Should I use the frozen method somehow?
>
>     I did do something similar some years back. But at the time I removed
>     the stuff I had drawn on the figure. I would like to avoid this for
>     two reasons: 1) Thread safety, I must be able to draw figures in
>     several simultaneous threads and 2) I really had to go into some
>     low-level details in matplotlib (not a show-stopper, but for
>     maintenance reasons I would like to keep the code as clear as
>     possible).
>
>     Best regards,
>     Jesper
>
>
> Jesper,
>
> An experimental feature that will be available in the upcoming v1.2.0
> release will be pickling support.  It is marked as experimental as there
> are plenty of untested edge cases, but it should be a huge step in the
> right direction for the feature that you and many others have asked
> for.  We certainly will welcome any and all feedback on what does and
> does not pickle well.
>
> Cheers!
> Ben Root

Some benchmarking would be useful as well.  Pickling/unpickling can be 
very slow.

Eric

Re: [Matplotlib-users] Saving figure instance for reuse

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

On Wed, Aug 15, 2012 at 5:40 AM, Jesper Larsen <jes...@gm...>wrote:

> Hi Matplotlib users
>
> I have an application where performance is critical and matplotlib is
> the performance bottleneck. I am making a lot of figures using the
> same basic setup of the figure. And from my profiling I can see that
> this basic setup accounts for most of the CPU time. Let us say that I
> make a given figure including some axes. My questions are:
>
> 1. Can I make a copy of this figure including axes (copy.deepcopy does
> not work on Figure objects) and use the copy for plotting on?
>
> 2. And how? Should I use the frozen method somehow?
>
> I did do something similar some years back. But at the time I removed
> the stuff I had drawn on the figure. I would like to avoid this for
> two reasons: 1) Thread safety, I must be able to draw figures in
> several simultaneous threads and 2) I really had to go into some
> low-level details in matplotlib (not a show-stopper, but for
> maintenance reasons I would like to keep the code as clear as
> possible).
>
> Best regards,
> Jesper
>
>
Jesper,

An experimental feature that will be available in the upcoming v1.2.0
release will be pickling support.  It is marked as experimental as there
are plenty of untested edge cases, but it should be a huge step in the
right direction for the feature that you and many others have asked for.
We certainly will welcome any and all feedback on what does and does not
pickle well.

Cheers!
Ben Root

Re: [Matplotlib-users] python question from matlab user

[Eric F. <ef...@ha...>]

On 2012/09/08 5:34 PM, Jody Klymak wrote:
>
>>
>> This is one of the big differences between python and matlab: in
>> matlab, if an m-file has changed within a session, the change is
>> immediately effective. The python "import" statement is very
>> different.
>
> Gotchya, thanks.
>
> So, while I'm being a bother:
>
> in Matlab, I often organize data in structures as:
>
> adcp.time [1xN] adcp.z  [Mx1] adcp.u  [MxN]
>
> where time is the x-axis, z the z-axis and u an array of values at
> each depth and time (an example chosen after Eric's heart).
>
> What is the recommended way to represent this in python?  I see the
> info about numpy structured arrays.  Is that it?  It also seems that
> Mx1 arrays are hard in python.  It also seems you need to preallocate
> the whole array, which isn't very flexible compared to how you can do
> it in Matlab.  Am I missing something?

Jody,

A structured array is probably overkill; it would require storing 
everything as MxN, which may not be necessary.

Most of the time, if you have something that is 1-D, you can just keep 
it in a 1-D array.  If you need adcp.time to behave as if it were MxN, 
you can just use it as-is, because numpy broadcasting will add 
dimensions to the left as needed.  If you need adcp.z to behave as if it 
were MxN, you can simply index it like this: adcp.z[:, np.newaxis].

Now, for the structure syntax, you can use a class, e.g.

class Data:
     pass

adcp = Data()
adcp.time = time
adcp.z = z
adcp.u = u

Now your adcp instance is just like the matlab structure.

This works, but you might want to use a more flexible container.  One 
variation on the Bunch is here:
http://currents.soest.hawaii.edu/hgstage/pycurrents/file/8bf05a53b326/system/misc.py.
It is fancier than you need for now, but illustrates the sort of thing 
you can do with python, and it will work fine even when you don't need 
all its features.  You could initialize it like this:

adcp = Bunch(time=time, z=z, u=u)

assuming, as before, that you already have individual numpy arrays 
called time, z, and u.  You can still tack on additional attributes, like

adcp.something_else = whatever

The Bunch allows access using the structure notation, and also using 
dictionary syntax, so adcp.u is the same as adcp['u'].  The dictionary 
syntax is particularly useful when automating operations, because you 
can easily iterate over a list of dictionary entries.

Regarding the need to pre-allocate: yes, matlab is slicker in this 
regard, and every now and then there is discussion about implementing 
equivalent behavior in numpy, or in an add-on module.

In many cases you can simply accumulate values in a list, and then at 
the end use an array constructor to make an ndarray from the list.

You can also use the numpy concatenate function, or its derivatives, but 
this usually makes sense only for gluing together small numbers of arrays.

Eric

>
> Thanks,   Jody
>

Re: [Matplotlib-users] python question from matlab user

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

> 
> This is one of the big differences between python and matlab: in matlab, 
> if an m-file has changed within a session, the change is immediately 
> effective. The python "import" statement is very different. 

Gotchya, thanks.  

So, while I'm being a bother:

in Matlab, I often organize data in structures as:

adcp.time [1xN]
adcp.z  [Mx1]
adcp.u  [MxN]

where time is the x-axis, z the z-axis and u an array of values at each depth and time (an example chosen after Eric's heart).  

What is the recommended way to represent this in python?  I see the info about numpy structured arrays.  Is that it?  It also seems that Mx1 arrays are hard in python.  It also seems you need to preallocate the whole array, which isn't very flexible compared to how you can do it in Matlab.  Am I missing something?

Thanks,   Jody



> 
>> 
>> Sorry for the chatter, and thanks for the pointers..
>> Cheers,   Jody
>> 
>> On Sep 8, 2012, at  6:18 AM, Jody Klymak <jk...@uv...
>> <mailto:jk...@uv...>> wrote:
>> 
>>> Hi all,
>>> 
>>> Thats what I thought too:
>>> 
>>> I have: jmkfigure.py:
>>> 
>>> ===============
>>> from pylab import *
>>> 
>>> def jmkfigure():
>>>    rc('figure',figsize=(3+3/8,8.5/2),dpi=96)
>>>    rc('font',size=9);
>>> ===========
>>> 
>>> and test.py:
>>> 
>>> =========
>>> from pylab import *
>>> 
>>> from jmkfigure import *
>>> 
>>> jmkfigure()
>>> figure(1)
>>> plot([1,2,3]);
>>> 
>>> show()
>>> ==============
>>> 
>>>>>> run test.py
>>> 
>>> yields a traceback ending w/:
>>> 
>>> ===========
>>> Users/jklymak/teaching/Phy411/project/jmkfigure.py in jmkfigure()
>>>      1 from pylab import *
>>> ----> 2
>>>      3 def jmkfigure():
>>>      4     rc('figure',figsize=(3+3/8,8.5/2),dpi=96)
>>>      5     rc('font',size=9);
>>> 
>>> NameError: global name 'rc' is not defined
>>> ========
>>> 
>>> Same error if I just import "rc" from matplot lib....
>>> 
>>> Is it some strange set up problem?  If I put the same def in test.py
>>> it works fine...
>>> 
>>> Thanks,  Jody
>>> 
>>> On Sep 7, 2012, at  22:52 PM, Paul Tremblay <pau...@gm...
>>> <mailto:pau...@gm...>> wrote:
>>> 
>>>> in your jmkfile.py you should have
>>>> 
>>>> from  pylab  import  *
>>>> 
>>>> Paul
>>>> 
>>>> 
>>>> On 9/8/12 12:45 AM, Jody Klymak wrote:
>>>>> Hi All,
>>>>> 
>>>>> Sorry to ask a dumb python newbie question, but the problem arose while reading the matplotlib documentation, and an hour or so on the internet didnt' help, so I felt it was fair-ish game to post here.
>>>>> 
>>>>> Inhttp://matplotlib.sourceforge.net/examples/pylab_examples/customize_rc.html  it says:
>>>>> """
>>>>> If you like to work interactively, and need to create different sets
>>>>> of defaults for figures (eg one set of defaults for publication, one
>>>>> set for interactive exploration), you may want to define some
>>>>> functions in a custom module that set the defaults, eg
>>>>> 
>>>>> def set_pub():
>>>>>     rc('font', weight='bold')    # bold fonts are easier to see
>>>>> 
>>>>> Then as you are working interactively, you just need to do
>>>>> 
>>>>>>>> set_pub()
>>>>> """
>>>>> 
>>>>> Which I thought was great, because I'd like to have some presets for different journals.  However, saving the def into a file (jmkfigure.py) and calling
>>>>> 
>>>>> from jmkfigure import *
>>>>> 
>>>>> set_pub()
>>>>> 
>>>>> yields the error: "NameError: global name 'rc' is not defined"
>>>>> 
>>>>> I tried importing matplotlib and rc into jmkfigure.py, but to no avail.
>>>>> 
>>>>> I appreciate this is a scoping issue with python, but I can't figure out how to set rc from within an external module.
>>>>> 
>>>>> Thanks for any help,
>>>>> 
>>>>> Cheers,   Jody
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond.
>>>> Discussions
>>>> will include endpoint security, mobile security and the latest in
>>>> malware
>>>> threats.
>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>>>> Matplotlib-users mailing list
>>>> Mat...@li...
>>>> <mailto:Mat...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>> 
>>> --
>>> Jody Klymak
>>> http://web.uvic.ca/~jklymak/
>>> 
>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> <mailto:Mat...@li...>
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>> 
>> --
>> Jody Klymak
>> http://web.uvic.ca/~jklymak/
>> 
>> 
>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> 
>> 
>> 
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>> 
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

--
Jody Klymak    
http://web.uvic.ca/~jklymak/

Re: [Matplotlib-users] python question from matlab user

[Eric F. <ef...@ha...>]

On 2012/09/08 3:50 AM, Jody Klymak wrote:
> Ack, OK, to answer my own question...
>
> Somehow ipython was caching the definition of jmkfigure, so changing the
> module in the jmkfigure.py file did not actually change the version
> ipython was using. Running a new version of ipython, it worked fine.

Jody,

This is one of the big differences between python and matlab: in matlab, 
if an m-file has changed within a session, the change is immediately 
effective. The python "import" statement is very different.  If a module 
has been imported, then a subsequent "import" of it does not re-read the 
file, even if it has changed. There is a "reload" builtin function that 
will re-read a file, but it is rarely used.  It reloads only the 
specified module, not modules that use it.  Ipython has a recursive 
dreload (for deep reload) function, but I don't use that, either; I just 
do what you did, start a new instance of ipython.

In ipython, the %run magic is useful for developing and modifying a 
single module or script at at time, making changes and testing without 
restarting ipython.

Eric

>
> Sorry for the chatter, and thanks for the pointers..
> Cheers,   Jody
>
> On Sep 8, 2012, at  6:18 AM, Jody Klymak <jk...@uv...
> <mailto:jk...@uv...>> wrote:
>
>> Hi all,
>>
>> Thats what I thought too:
>>
>> I have: jmkfigure.py:
>>
>> ===============
>> from pylab import *
>>
>> def jmkfigure():
>>     rc('figure',figsize=(3+3/8,8.5/2),dpi=96)
>>     rc('font',size=9);
>> ===========
>>
>> and test.py:
>>
>> =========
>> from pylab import *
>>
>> from jmkfigure import *
>>
>> jmkfigure()
>> figure(1)
>> plot([1,2,3]);
>>
>> show()
>> ==============
>>
>> >>> run test.py
>>
>> yields a traceback ending w/:
>>
>> ===========
>> Users/jklymak/teaching/Phy411/project/jmkfigure.py in jmkfigure()
>>       1 from pylab import *
>> ----> 2
>>       3 def jmkfigure():
>>       4     rc('figure',figsize=(3+3/8,8.5/2),dpi=96)
>>       5     rc('font',size=9);
>>
>> NameError: global name 'rc' is not defined
>> ========
>>
>> Same error if I just import "rc" from matplot lib....
>>
>> Is it some strange set up problem?  If I put the same def in test.py
>> it works fine...
>>
>> Thanks,  Jody
>>
>> On Sep 7, 2012, at  22:52 PM, Paul Tremblay <pau...@gm...
>> <mailto:pau...@gm...>> wrote:
>>
>>> in your jmkfile.py you should have
>>>
>>> from  pylab  import  *
>>>
>>> Paul
>>>
>>>
>>> On 9/8/12 12:45 AM, Jody Klymak wrote:
>>>> Hi All,
>>>>
>>>> Sorry to ask a dumb python newbie question, but the problem arose while reading the matplotlib documentation, and an hour or so on the internet didnt' help, so I felt it was fair-ish game to post here.
>>>>
>>>> Inhttp://matplotlib.sourceforge.net/examples/pylab_examples/customize_rc.html  it says:
>>>> """
>>>> If you like to work interactively, and need to create different sets
>>>> of defaults for figures (eg one set of defaults for publication, one
>>>> set for interactive exploration), you may want to define some
>>>> functions in a custom module that set the defaults, eg
>>>>
>>>> def set_pub():
>>>>      rc('font', weight='bold')    # bold fonts are easier to see
>>>>
>>>> Then as you are working interactively, you just need to do
>>>>
>>>>>>> set_pub()
>>>> """
>>>>
>>>> Which I thought was great, because I'd like to have some presets for different journals.  However, saving the def into a file (jmkfigure.py) and calling
>>>>
>>>> from jmkfigure import *
>>>>
>>>> set_pub()
>>>>
>>>> yields the error: "NameError: global name 'rc' is not defined"
>>>>
>>>> I tried importing matplotlib and rc into jmkfigure.py, but to no avail.
>>>>
>>>> I appreciate this is a scoping issue with python, but I can't figure out how to set rc from within an external module.
>>>>
>>>> Thanks for any help,
>>>>
>>>> Cheers,   Jody
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond.
>>> Discussions
>>> will include endpoint security, mobile security and the latest in
>>> malware
>>> threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> <mailto:Mat...@li...>
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>> --
>> Jody Klymak
>> http://web.uvic.ca/~jklymak/
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats.
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> <mailto:Mat...@li...>
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
> --
> Jody Klymak
> http://web.uvic.ca/~jklymak/
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Re: [Matplotlib-users] python question from matlab user

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

Ack, OK, to answer my own question...

Somehow ipython was caching the definition of jmkfigure, so changing the module in the jmkfigure.py file did not actually change the version ipython was using. Running a new version of ipython, it worked fine.  

Sorry for the chatter, and thanks for the pointers..
 
Cheers,   Jody

On Sep 8, 2012, at  6:18 AM, Jody Klymak <jk...@uv...> wrote:

> Hi all,
> 
> Thats what I thought too:
> 
> I have: jmkfigure.py:
> 
> ===============
> from pylab import *
> 
> def jmkfigure():
>     rc('figure',figsize=(3+3/8,8.5/2),dpi=96)
>     rc('font',size=9);
> ===========
> 
> and test.py:
> 
> =========
> from pylab import *
> 
> from jmkfigure import *
> 
> jmkfigure()
> figure(1)
> plot([1,2,3]);
> 
> show()
> ==============
> 
> >>> run test.py
> 
> yields a traceback ending w/:
> 
> ===========
> Users/jklymak/teaching/Phy411/project/jmkfigure.py in jmkfigure()
>       1 from pylab import *
> ----> 2 
>       3 def jmkfigure():
>       4     rc('figure',figsize=(3+3/8,8.5/2),dpi=96)
>       5     rc('font',size=9);
> 
> NameError: global name 'rc' is not defined
> ========
> 
> Same error if I just import "rc" from matplot lib....
> 
> Is it some strange set up problem?  If I put the same def in test.py it works fine...
> 
> Thanks,  Jody
> 
> On Sep 7, 2012, at  22:52 PM, Paul Tremblay <pau...@gm...> wrote:
> 
>> in your jmkfile.py you should have
>> 
>> from pylab import *
>> 
>> Paul
>> 
>> 
>> On 9/8/12 12:45 AM, Jody Klymak wrote:
>>> Hi All,
>>> 
>>> Sorry to ask a dumb python newbie question, but the problem arose while reading the matplotlib documentation, and an hour or so on the internet didnt' help, so I felt it was fair-ish game to post here. 
>>> 
>>> In http://matplotlib.sourceforge.net/examples/pylab_examples/customize_rc.html it says:
>>> """
>>> If you like to work interactively, and need to create different sets
>>> of defaults for figures (eg one set of defaults for publication, one
>>> set for interactive exploration), you may want to define some
>>> functions in a custom module that set the defaults, eg
>>> 
>>> def set_pub():
>>>     rc('font', weight='bold')    # bold fonts are easier to see
>>> 
>>> Then as you are working interactively, you just need to do
>>> 
>>>>>> set_pub()
>>> """
>>> 
>>> Which I thought was great, because I'd like to have some presets for different journals.  However, saving the def into a file (jmkfigure.py) and calling 
>>> 
>>> from jmkfigure import *
>>> 
>>> set_pub()
>>> 
>>> yields the error: "NameError: global name 'rc' is not defined" 
>>> 
>>> I tried importing matplotlib and rc into jmkfigure.py, but to no avail.  
>>> 
>>> I appreciate this is a scoping issue with python, but I can't figure out how to set rc from within an external module.
>>> 
>>> Thanks for any help,
>>> 
>>> Cheers,   Jody
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and 
>> threat landscape has changed and how IT managers can respond. Discussions 
>> will include endpoint security, mobile security and the latest in malware 
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
> --
> Jody Klymak    
> http://web.uvic.ca/~jklymak/
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

--
Jody Klymak    
http://web.uvic.ca/~jklymak/

Re: [Matplotlib-users] python question from matlab user

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

Hi all,

Thats what I thought too:

I have: jmkfigure.py:

===============
from pylab import *

def jmkfigure():
    rc('figure',figsize=(3+3/8,8.5/2),dpi=96)
    rc('font',size=9);
===========

and test.py:

=========
from pylab import *

from jmkfigure import *

jmkfigure()
figure(1)
plot([1,2,3]);

show()
==============

>>> run test.py

yields a traceback ending w/:

===========
Users/jklymak/teaching/Phy411/project/jmkfigure.py in jmkfigure()
      1 from pylab import *
----> 2 
      3 def jmkfigure():
      4     rc('figure',figsize=(3+3/8,8.5/2),dpi=96)
      5     rc('font',size=9);

NameError: global name 'rc' is not defined
========

Same error if I just import "rc" from matplot lib....

Is it some strange set up problem?  If I put the same def in test.py it works fine...

Thanks,  Jody

On Sep 7, 2012, at  22:52 PM, Paul Tremblay <pau...@gm...> wrote:

> in your jmkfile.py you should have
> 
> from pylab import *
> 
> Paul
> 
> 
> On 9/8/12 12:45 AM, Jody Klymak wrote:
>> Hi All,
>> 
>> Sorry to ask a dumb python newbie question, but the problem arose while reading the matplotlib documentation, and an hour or so on the internet didnt' help, so I felt it was fair-ish game to post here. 
>> 
>> In http://matplotlib.sourceforge.net/examples/pylab_examples/customize_rc.html it says:
>> """
>> If you like to work interactively, and need to create different sets
>> of defaults for figures (eg one set of defaults for publication, one
>> set for interactive exploration), you may want to define some
>> functions in a custom module that set the defaults, eg
>> 
>> def set_pub():
>>     rc('font', weight='bold')    # bold fonts are easier to see
>> 
>> Then as you are working interactively, you just need to do
>> 
>>>>> set_pub()
>> """
>> 
>> Which I thought was great, because I'd like to have some presets for different journals.  However, saving the def into a file (jmkfigure.py) and calling 
>> 
>> from jmkfigure import *
>> 
>> set_pub()
>> 
>> yields the error: "NameError: global name 'rc' is not defined" 
>> 
>> I tried importing matplotlib and rc into jmkfigure.py, but to no avail.  
>> 
>> I appreciate this is a scoping issue with python, but I can't figure out how to set rc from within an external module.
>> 
>> Thanks for any help,
>> 
>> Cheers,   Jody
>> 
>> 
>> 
>> 
>> 
>> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

--
Jody Klymak    
http://web.uvic.ca/~jklymak/

Re: [Matplotlib-users] python question from matlab user

[Eric F. <ef...@ha...>]

On 2012/09/07 7:52 PM, Paul Tremblay wrote:
> in your jmkfile.py you should have
>
> from  pylab  import  *

Or to be more pythonic, import only what you actually need in a given 
module, e.g.,

from matplotlib import rc

Eric

>
> Paul
>
>
>
> On 9/8/12 12:45 AM, Jody Klymak wrote:
>> Hi All,
>>
>> Sorry to ask a dumb python newbie question, but the problem arose while reading the matplotlib documentation, and an hour or so on the internet didnt' help, so I felt it was fair-ish game to post here.
>>
>> Inhttp://matplotlib.sourceforge.net/examples/pylab_examples/customize_rc.html  it says:
>> """
>> If you like to work interactively, and need to create different sets
>> of defaults for figures (eg one set of defaults for publication, one
>> set for interactive exploration), you may want to define some
>> functions in a custom module that set the defaults, eg
>>
>> def set_pub():
>>      rc('font', weight='bold')    # bold fonts are easier to see
>>
>> Then as you are working interactively, you just need to do
>>
>>>>> set_pub()
>> """
>>
>> Which I thought was great, because I'd like to have some presets for different journals.  However, saving the def into a file (jmkfigure.py) and calling
>>
>> from jmkfigure import *
>>
>> set_pub()
>>
>> yields the error: "NameError: global name 'rc' is not defined"
>>
>> I tried importing matplotlib and rc into jmkfigure.py, but to no avail.
>>
>> I appreciate this is a scoping issue with python, but I can't figure out how to set rc from within an external module.
>>
>> Thanks for any help,
>>
>> Cheers,   Jody
>>
>>
>>
>>
>>
>>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Re: [Matplotlib-users] python question from matlab user

[Paul T. <pau...@gm...>]

in your jmkfile.py you should have

from  pylab  import  *

Paul



On 9/8/12 12:45 AM, Jody Klymak wrote:
> Hi All,
>
> Sorry to ask a dumb python newbie question, but the problem arose while reading the matplotlib documentation, and an hour or so on the internet didnt' help, so I felt it was fair-ish game to post here.
>
> In http://matplotlib.sourceforge.net/examples/pylab_examples/customize_rc.html it says:
> """
> If you like to work interactively, and need to create different sets
> of defaults for figures (eg one set of defaults for publication, one
> set for interactive exploration), you may want to define some
> functions in a custom module that set the defaults, eg
>
> def set_pub():
>      rc('font', weight='bold')    # bold fonts are easier to see
>
> Then as you are working interactively, you just need to do
>
>>>> set_pub()
> """
>
> Which I thought was great, because I'd like to have some presets for different journals.  However, saving the def into a file (jmkfigure.py) and calling
>
> from jmkfigure import *
>
> set_pub()
>
> yields the error: "NameError: global name 'rc' is not defined"
>
> I tried importing matplotlib and rc into jmkfigure.py, but to no avail.
>
> I appreciate this is a scoping issue with python, but I can't figure out how to set rc from within an external module.
>
> Thanks for any help,
>
> Cheers,   Jody
>
>
>
>
>
>

[Matplotlib-users] python question from matlab user

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

Hi All,

Sorry to ask a dumb python newbie question, but the problem arose while reading the matplotlib documentation, and an hour or so on the internet didnt' help, so I felt it was fair-ish game to post here. 

In http://matplotlib.sourceforge.net/examples/pylab_examples/customize_rc.html it says:
"""
If you like to work interactively, and need to create different sets
of defaults for figures (eg one set of defaults for publication, one
set for interactive exploration), you may want to define some
functions in a custom module that set the defaults, eg

def set_pub():
    rc('font', weight='bold')    # bold fonts are easier to see

Then as you are working interactively, you just need to do

>>> set_pub()
"""

Which I thought was great, because I'd like to have some presets for different journals.  However, saving the def into a file (jmkfigure.py) and calling 

from jmkfigure import *

set_pub()

yields the error: "NameError: global name 'rc' is not defined" 

I tried importing matplotlib and rc into jmkfigure.py, but to no avail.  

I appreciate this is a scoping issue with python, but I can't figure out how to set rc from within an external module.

Thanks for any help,

Cheers,   Jody

Re: [Matplotlib-users] Using the lasso tool when file is not main

[Mark B. <mar...@gm...>]

Thanks Ben, that solved my issue. I guess I got thrown off because the
plot stayed open, as you described. It's hard to troubleshoot when you
don't get any errors. In the future I will attach all of my objects.
-Mark

On Fri, Sep 7, 2012 at 12:03 PM, Benjamin Root <ben...@ou...> wrote:
> I think I see your problem... see below:
>
>
> class start_lasso():
>     def __init__(self):
>         data = [Datum(*xy) for xy in rand(100, 2)]
>
>         fig = figure()
>         ax = fig.add_subplot(111, xlim=(0,1), ylim=(0,1),
> autoscale_on=False)
>         lman = LassoManager(ax, data)
>         show()
>
> You aren't saving any of the objects created in the "start_lasso" class to
> your start_lasso object.  Luckily, with the way pyplot works, the figure
> object your create gets implicitly saved to the "pyplot state manager" (a
> sort of smart global location for the figure objects), and the axes object
> gets implicitly attached to the figure object.  Therefore, when the python
> execution goes out of this scope, the figure object and the axes do not get
> garbage-collected.  However, the lasso widget that gets created and all the
> callbacks that were attached are all done with weak references to the figure
> and axes.  So when you leave this scope, the LassoManager no longer exists
> and the callback fails to execute (as designed).
>
> So, make sure that at least lman (and possibly fig and ax) gets saved to the
> start_lasso object to solve that part of the problem.  Next, you don't save
> the start_lasso object your create anywhere, so even if you saved lman to
> start_lasso, the start_lasso object gets garbage-collected anyway as a
> temporary.
>
> I hope this is clear.  Let me know if you still have more issues.
>
> Cheers!
> Ben Root
>

Re: [Matplotlib-users] Using the lasso tool when file is not main

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

I think I see your problem... see below:


class start_lasso():
    def __init__(self):
        data = [Datum(*xy) for xy in rand(100, 2)]

        fig = figure()
        ax = fig.add_subplot(111, xlim=(0,1), ylim=(0,1),
autoscale_on=False)
        lman = LassoManager(ax, data)
        show()

You aren't saving any of the objects created in the "start_lasso" class to
your start_lasso object.  Luckily, with the way pyplot works, the figure
object your create gets implicitly saved to the "pyplot state manager" (a
sort of smart global location for the figure objects), and the axes object
gets implicitly attached to the figure object.  Therefore, when the python
execution goes out of this scope, the figure object and the axes do not get
garbage-collected.  However, the lasso widget that gets created and all the
callbacks that were attached are all done with weak references to the
figure and axes.  So when you leave this scope, the LassoManager no longer
exists and the callback fails to execute (as designed).

So, make sure that at least lman (and possibly fig and ax) gets saved to
the start_lasso object to solve that part of the problem.  Next, you don't
save the start_lasso object your create anywhere, so even if you saved lman
to start_lasso, the start_lasso object gets garbage-collected anyway as a
temporary.

I hope this is clear.  Let me know if you still have more issues.

Cheers!
Ben Root

Re: [Matplotlib-users] MemoryError with NetCDF

[Ethan G. <eth...@gm...>]

On Sep 7, 2012, at 11:04 AM, Eric Firing wrote:

> On 2012/09/07 4:00 AM, Benjamin Root wrote:
>> 
>> 
>> On Fri, Sep 7, 2012 at 9:49 AM, Shahar Shani-Kadmiel
>> <ka...@po... <mailto:ka...@po...>> wrote:
>> 
>>    On Sep 7, 2012, at 4:25 PM, Benjamin Root wrote:
>> 
>>> 
>>> 
>>>    On Fri, Sep 7, 2012 at 8:44 AM, Shahar Shani-Kadmiel
>>>    <ka...@po... <mailto:ka...@po...>> wrote:
>>> 
> 
<snip>

> Normalization has to handle all sorts of inputs--masked or not, all 
> sorts of numbers, scalar or array--and it is much easier to do this 
> efficiently if all these possibilities are reduced to a very few at the 
> start.  Specifically, it needs to supply a copy of the input (so that 
> normalization doesn't change the original) in a floating point masked 
> array, using float32 if possible for space efficiency.  It needs to keep 
> track of whether the input was a scalar, so that normalization can 
> return a scalar when given a scalar input.
> 
> Eric

Another option as I understand it is to pass in a 1D (greyscale) or 3d (color) array (where the 3rd dimension is RGB and optionally A) of type uint8(?). This array does not need to get normalized, it will be displayed as raw pixel values.  I don't remember if you also have to specifically tell it not to normalize the data. 

But the easier answer for your case would probably be imshow(data[::10,::10]) which will take every 10th element in x and y thus reducing the size by a factor of 100 (depending on the size of your data you could use ::2 or ::50, etc)

Ethan

Re: [Matplotlib-users] MemoryError with NetCDF

[Eric F. <ef...@ha...>]

On 2012/09/07 4:00 AM, Benjamin Root wrote:
>
>
> On Fri, Sep 7, 2012 at 9:49 AM, Shahar Shani-Kadmiel
> <ka...@po... <mailto:ka...@po...>> wrote:
>
>     On Sep 7, 2012, at 4:25 PM, Benjamin Root wrote:
>
>>
>>
>>     On Fri, Sep 7, 2012 at 8:44 AM, Shahar Shani-Kadmiel
>>     <ka...@po... <mailto:ka...@po...>> wrote:
>>
>>         1. an ipython session is invoked with qtconsole --pylab
>>         2. I load a large NetCDF grid (Grid file format: nf (# 18) GMT
>>         netCDF format (float)  (COARDS-compliant) [DEFAULT]), approx.
>>         1.15 GB
>>         3. I then try to plot with imshow the data
>>
>>         added below are the lines leading up to the error and the
>>         error itself.
>>
>>
>>         This is running on OS X 10.7.4 with a recently installed EPD 7.3.
>>
>>
>>         {code}
>>         from scipy.io <http://scipy.io/> import netcdf_file as netcdf
>>         data =
>>         netcdf('srtm_43_44_05_06_07_08.grd','r').variables['z'][::-1]
>>
>>         fig, ax = subplots()
>>
>>         data.shape
>>         Out[5]: (24004, 12002)
>>
>>         im = ax.imshow(data,
>>         aspect=((data.shape[1])/float(data.shape[0])),
>>         interpolation='none')
>>         ---------------------------------------------------------------------------
>>         MemoryError                               Traceback (most
>>         recent call last)
>>         <ipython-input-6-f92e4c4c63b5> in <module>()
>>         ----> 1 im = ax.imshow(data,
>>         aspect=((data.shape[1])/float(data.shape[0])),
>>         interpolation='none')
>>
>>         /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/axes.py
>>         in imshow(self, X, cmap, norm, aspect, interpolation, alpha,
>>         vmin, vmax, origin, extent, shape, filternorm, filterrad,
>>         imlim, resample, url, **kwargs)
>>            6743             im.set_clim(vmin, vmax)
>>            6744         else:
>>         -> 6745             im.autoscale_None()
>>            6746         im.set_url(url)
>>            6747
>>
>>         /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cm.py
>>         in autoscale_None(self)
>>             281         if self._A is None:
>>             282             raise TypeError('You must first set_array
>>         for mappable')
>>         --> 283         self.norm.autoscale_None(self._A)
>>             284         self.changed()
>>             285
>>
>>         /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py
>>         in autoscale_None(self, A)
>>             889         ' autoscale only None-valued vmin or vmax'
>>             890         if self.vmin is None:
>>         --> 891             self.vmin = ma.min(A)
>>             892         if self.vmax is None:
>>             893             self.vmax = ma.max(A)
>>
>>         /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
>>         in min(obj, axis, out, fill_value)
>>            5873 def min(obj, axis=None, out=None, fill_value=None):
>>            5874     try:
>>         -> 5875         return obj.min(axis=axis,
>>         fill_value=fill_value, out=out)
>>            5876     except (AttributeError, TypeError):
>>            5877         # If obj doesn't have a max method,
>>
>>         /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
>>         in min(self, axis, out, fill_value)
>>            5054         # No explicit output
>>            5055         if out is None:
>>         -> 5056             result =
>>         self.filled(fill_value).min(axis=axis, out=out).view(type(self))
>>            5057             if result.ndim:
>>            5058                 # Set the mask
>>
>>         /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
>>         in filled(self, fill_value)
>>            3388             return self._data
>>            3389         else:
>>         -> 3390             result = self._data.copy()
>>            3391             try:
>>            3392                 np.putmask(result, m, fill_value)
>>
>>         MemoryError:
>>         {/code}
>>
>>
>>     This is more a NumPy issue than anything else.  We need to know
>>     the min and the max of the array in order to automatically scale
>>     the colormap for display.  Therefore, we query the array object
>>     for its min/max.  Because we support masked arrays, the array is
>>     first cast as a masked array, and then these queries are done.
>>
>>     It appears that in numpy's masked array module, it calculates the
>>     array's min by making a copy of itself first.  I would have
>>     figured that it would have done its task differently.  In the
>>     meantime, I suspect you can work around this problem by explicitly
>>     setting the vmin/vmax keyword arguments to imshow if you know
>>     them.  Therefore, there should be no need to determine the array's
>>     min/max in this inefficient manner.
>>
>>     Ben Root
>>
>
>     Hi Ben,
>     I tried adding vmin & vmax the the imshow call but I still get a
>     MemoryError.
>     The grid file is 1.15 GB and I have ~4.5 out of 8 GB of memory
>     available when I launch ipython, 3.5 when I execute imshow and 2
>     when I execute plt.draw().

mpl simply is not designed for image-type operations on huge arrays, 
vastly larger than what can be displayed.  It is up to the user to 
down-sample or otherwise reduce the size of the array fed to imshow.

>
>
> Well, it looks like setting vmin/vmax helped, because your traceback

Did a new traceback get posted in a message that was not sent to the 
list?  I found only the original traceback.

> shows that the code made significant progress.  The issue here is that
> the process_value() method doesn't make a lot of sense.  I am not sure
> what is the rationale behind its logic.  Hopefully, someone else can
> chime in with an explanation of what is going on.

Normalization has to handle all sorts of inputs--masked or not, all 
sorts of numbers, scalar or array--and it is much easier to do this 
efficiently if all these possibilities are reduced to a very few at the 
start.  Specifically, it needs to supply a copy of the input (so that 
normalization doesn't change the original) in a floating point masked 
array, using float32 if possible for space efficiency.  It needs to keep 
track of whether the input was a scalar, so that normalization can 
return a scalar when given a scalar input.

Eric

>
> In the meantime, are you using a 32 or 64-bit machine?
>
> Ben Root
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Re: [Matplotlib-users] MemoryError with NetCDF

[Shahar Shani-K. <ka...@po...>]

On Sep 7, 2012, at 5:00 PM, Benjamin Root <ben...@ou...> wrote:

> 
> 
> On Fri, Sep 7, 2012 at 9:49 AM, Shahar Shani-Kadmiel <ka...@po...> wrote:
> On Sep 7, 2012, at 4:25 PM, Benjamin Root wrote:
> 
>> 
>> 
>> On Fri, Sep 7, 2012 at 8:44 AM, Shahar Shani-Kadmiel <ka...@po...> wrote:
>> 1. an ipython session is invoked with qtconsole --pylab
>> 2. I load a large NetCDF grid (Grid file format: nf (# 18) GMT netCDF format (float)  (COARDS-compliant) [DEFAULT]), approx. 1.15 GB
>> 3. I then try to plot with imshow the data
>> 
>> added below are the lines leading up to the error and the error itself.
>> 
>> 
>> This is running on OS X 10.7.4 with a recently installed EPD 7.3.
>> 
>> 
>> {code}
>> from scipy.io import netcdf_file as netcdf
>> data = netcdf('srtm_43_44_05_06_07_08.grd','r').variables['z'][::-1]
>> 
>> fig, ax = subplots()
>> 
>> data.shape
>> Out[5]: (24004, 12002)
>> 
>> im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])), interpolation='none')
>> ---------------------------------------------------------------------------
>> MemoryError                               Traceback (most recent call last)
>> <ipython-input-6-f92e4c4c63b5> in <module>()
>> ----> 1 im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])), interpolation='none')
>> 
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/axes.py in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)
>>    6743             im.set_clim(vmin, vmax)
>>    6744         else:
>> -> 6745             im.autoscale_None()
>>    6746         im.set_url(url)
>>    6747
>> 
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cm.py in autoscale_None(self)
>>     281         if self._A is None:
>>     282             raise TypeError('You must first set_array for mappable')
>> --> 283         self.norm.autoscale_None(self._A)
>>     284         self.changed()
>>     285
>> 
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py in autoscale_None(self, A)
>>     889         ' autoscale only None-valued vmin or vmax'
>>     890         if self.vmin is None:
>> --> 891             self.vmin = ma.min(A)
>>     892         if self.vmax is None:
>>     893             self.vmax = ma.max(A)
>> 
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in min(obj, axis, out, fill_value)
>>    5873 def min(obj, axis=None, out=None, fill_value=None):
>>    5874     try:
>> -> 5875         return obj.min(axis=axis, fill_value=fill_value, out=out)
>>    5876     except (AttributeError, TypeError):
>>    5877         # If obj doesn't have a max method,
>> 
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in min(self, axis, out, fill_value)
>>    5054         # No explicit output
>>    5055         if out is None:
>> -> 5056             result = self.filled(fill_value).min(axis=axis, out=out).view(type(self))
>>    5057             if result.ndim:
>>    5058                 # Set the mask
>> 
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in filled(self, fill_value)
>>    3388             return self._data
>>    3389         else:
>> -> 3390             result = self._data.copy()
>>    3391             try:
>>    3392                 np.putmask(result, m, fill_value)
>> 
>> MemoryError:
>> {/code}
>> 
>> This is more a NumPy issue than anything else.  We need to know the min and the max of the array in order to automatically scale the colormap for display.  Therefore, we query the array object for its min/max.  Because we support masked arrays, the array is first cast as a masked array, and then these queries are done.
>> 
>> It appears that in numpy's masked array module, it calculates the array's min by making a copy of itself first.  I would have figured that it would have done its task differently.  In the meantime, I suspect you can work around this problem by explicitly setting the vmin/vmax keyword arguments to imshow if you know them.  Therefore, there should be no need to determine the array's min/max in this inefficient manner.
>> 
>> Ben Root
>> 
> 
> Hi Ben,
> I tried adding vmin & vmax the the imshow call but I still get a MemoryError.
> The grid file is 1.15 GB and I have ~4.5 out of 8 GB of memory available when I launch ipython, 3.5 when I execute imshow and 2 when I execute plt.draw().
> 
> Well, it looks like setting vmin/vmax helped, because your traceback shows that the code made significant progress.  The issue here is that the process_value() method doesn't make a lot of sense.  I am not sure what is the rationale behind its logic.  Hopefully, someone else can chime in with an explanation of what is going on.
> 
> In the meantime, are you using a 32 or 64-bit machine?
> 
> Ben Root
> 

I am on a 64 bit machine but 32 bit distro of Enthought. 

Re: [Matplotlib-users] MemoryError with NetCDF

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

On Fri, Sep 7, 2012 at 9:49 AM, Shahar Shani-Kadmiel <ka...@po...
> wrote:

> On Sep 7, 2012, at 4:25 PM, Benjamin Root wrote:
>
>
>
> On Fri, Sep 7, 2012 at 8:44 AM, Shahar Shani-Kadmiel <
> ka...@po...> wrote:
>
>> 1. an ipython session is invoked with qtconsole --pylab
>> 2. I load a large NetCDF grid (Grid file format: nf (# 18) GMT netCDF
>> format (float)  (COARDS-compliant) [DEFAULT]), approx. 1.15 GB
>> 3. I then try to plot with imshow the data
>>
>> added below are the lines leading up to the error and the error itself.
>>
>>
>> This is running on OS X 10.7.4 with a recently installed EPD 7.3.
>>
>>
>> {code}
>> from scipy.io import netcdf_file as netcdf
>> data = netcdf('srtm_43_44_05_06_07_08.grd','r').variables['z'][::-1]
>>
>> fig, ax = subplots()
>>
>> data.shape
>> Out[5]: (24004, 12002)
>>
>> im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])),
>> interpolation='none')
>>
>> ---------------------------------------------------------------------------
>> MemoryError                               Traceback (most recent call
>> last)
>> <ipython-input-6-f92e4c4c63b5> in <module>()
>> ----> 1 im = ax.imshow(data,
>> aspect=((data.shape[1])/float(data.shape[0])), interpolation='none')
>>
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/axes.py
>> in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax,
>> origin, extent, shape, filternorm, filterrad, imlim, resample, url,
>> **kwargs)
>>    6743             im.set_clim(vmin, vmax)
>>    6744         else:
>> -> 6745             im.autoscale_None()
>>    6746         im.set_url(url)
>>    6747
>>
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cm.py
>> in autoscale_None(self)
>>     281         if self._A is None:
>>     282             raise TypeError('You must first set_array for
>> mappable')
>> --> 283         self.norm.autoscale_None(self._A)
>>     284         self.changed()
>>     285
>>
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py
>> in autoscale_None(self, A)
>>     889         ' autoscale only None-valued vmin or vmax'
>>     890         if self.vmin is None:
>> --> 891             self.vmin = ma.min(A)
>>     892         if self.vmax is None:
>>     893             self.vmax = ma.max(A)
>>
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
>> in min(obj, axis, out, fill_value)
>>    5873 def min(obj, axis=None, out=None, fill_value=None):
>>    5874     try:
>> -> 5875         return obj.min(axis=axis, fill_value=fill_value, out=out)
>>    5876     except (AttributeError, TypeError):
>>    5877         # If obj doesn't have a max method,
>>
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
>> in min(self, axis, out, fill_value)
>>    5054         # No explicit output
>>    5055         if out is None:
>> -> 5056             result = self.filled(fill_value).min(axis=axis,
>> out=out).view(type(self))
>>    5057             if result.ndim:
>>    5058                 # Set the mask
>>
>> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc
>> in filled(self, fill_value)
>>    3388             return self._data
>>    3389         else:
>> -> 3390             result = self._data.copy()
>>    3391             try:
>>    3392                 np.putmask(result, m, fill_value)
>>
>> MemoryError:
>> {/code}
>>
>
> This is more a NumPy issue than anything else.  We need to know the min
> and the max of the array in order to automatically scale the colormap for
> display.  Therefore, we query the array object for its min/max.  Because we
> support masked arrays, the array is first cast as a masked array, and then
> these queries are done.
>
> It appears that in numpy's masked array module, it calculates the array's
> min by making a copy of itself first.  I would have figured that it would
> have done its task differently.  In the meantime, I suspect you can work
> around this problem by explicitly setting the vmin/vmax keyword arguments
> to imshow if you know them.  Therefore, there should be no need to
> determine the array's min/max in this inefficient manner.
>
> Ben Root
>
>
> Hi Ben,
> I tried adding vmin & vmax the the imshow call but I still get a
> MemoryError.
> The grid file is 1.15 GB and I have ~4.5 out of 8 GB of memory available
> when I launch ipython, 3.5 when I execute imshow and 2 when I execute
> plt.draw().
>

Well, it looks like setting vmin/vmax helped, because your traceback shows
that the code made significant progress.  The issue here is that the
process_value() method doesn't make a lot of sense.  I am not sure what is
the rationale behind its logic.  Hopefully, someone else can chime in with
an explanation of what is going on.

In the meantime, are you using a 32 or 64-bit machine?

Ben Root

Re: [Matplotlib-users] MemoryError with NetCDF

[Shahar Shani-K. <ka...@po...>]

On Sep 7, 2012, at 4:25 PM, Benjamin Root wrote:

> 
> 
> On Fri, Sep 7, 2012 at 8:44 AM, Shahar Shani-Kadmiel <ka...@po...> wrote:
> 1. an ipython session is invoked with qtconsole --pylab
> 2. I load a large NetCDF grid (Grid file format: nf (# 18) GMT netCDF format (float)  (COARDS-compliant) [DEFAULT]), approx. 1.15 GB
> 3. I then try to plot with imshow the data
> 
> added below are the lines leading up to the error and the error itself.
> 
> 
> This is running on OS X 10.7.4 with a recently installed EPD 7.3.
> 
> 
> {code}
> from scipy.io import netcdf_file as netcdf
> data = netcdf('srtm_43_44_05_06_07_08.grd','r').variables['z'][::-1]
> 
> fig, ax = subplots()
> 
> data.shape
> Out[5]: (24004, 12002)
> 
> im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])), interpolation='none')
> ---------------------------------------------------------------------------
> MemoryError                               Traceback (most recent call last)
> <ipython-input-6-f92e4c4c63b5> in <module>()
> ----> 1 im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])), interpolation='none')
> 
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/axes.py in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)
>    6743             im.set_clim(vmin, vmax)
>    6744         else:
> -> 6745             im.autoscale_None()
>    6746         im.set_url(url)
>    6747
> 
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cm.py in autoscale_None(self)
>     281         if self._A is None:
>     282             raise TypeError('You must first set_array for mappable')
> --> 283         self.norm.autoscale_None(self._A)
>     284         self.changed()
>     285
> 
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py in autoscale_None(self, A)
>     889         ' autoscale only None-valued vmin or vmax'
>     890         if self.vmin is None:
> --> 891             self.vmin = ma.min(A)
>     892         if self.vmax is None:
>     893             self.vmax = ma.max(A)
> 
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in min(obj, axis, out, fill_value)
>    5873 def min(obj, axis=None, out=None, fill_value=None):
>    5874     try:
> -> 5875         return obj.min(axis=axis, fill_value=fill_value, out=out)
>    5876     except (AttributeError, TypeError):
>    5877         # If obj doesn't have a max method,
> 
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in min(self, axis, out, fill_value)
>    5054         # No explicit output
>    5055         if out is None:
> -> 5056             result = self.filled(fill_value).min(axis=axis, out=out).view(type(self))
>    5057             if result.ndim:
>    5058                 # Set the mask
> 
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in filled(self, fill_value)
>    3388             return self._data
>    3389         else:
> -> 3390             result = self._data.copy()
>    3391             try:
>    3392                 np.putmask(result, m, fill_value)
> 
> MemoryError:
> {/code}
> 
> This is more a NumPy issue than anything else.  We need to know the min and the max of the array in order to automatically scale the colormap for display.  Therefore, we query the array object for its min/max.  Because we support masked arrays, the array is first cast as a masked array, and then these queries are done.
> 
> It appears that in numpy's masked array module, it calculates the array's min by making a copy of itself first.  I would have figured that it would have done its task differently.  In the meantime, I suspect you can work around this problem by explicitly setting the vmin/vmax keyword arguments to imshow if you know them.  Therefore, there should be no need to determine the array's min/max in this inefficient manner.
> 
> Ben Root
> 

Hi Ben,
I tried adding vmin & vmax the the imshow call but I still get a MemoryError.
The grid file is 1.15 GB and I have ~4.5 out of 8 GB of memory available when I launch ipython, 3.5 when I execute imshow and 2 when I execute plt.draw().

im = ax.imshow(data, aspect=((data.shape[1])/float(data.shape[0])), interpolation=None, vmin=-400., vmax=3000.)

plt.draw()
---------------------------------------------------------------------------
MemoryError                               Traceback (most recent call last)
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53     def draw_wrapper(artist, renderer, *args, **kwargs):
     54         before(artist, renderer)
---> 55         draw(artist, renderer, *args, **kwargs)
     56         after(artist, renderer)
     57 

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/figure.py in draw(self, renderer)
    882         dsu.sort(key=itemgetter(0))
    883         for zorder, func, args in dsu:
--> 884             func(*args)
    885 
    886         renderer.close_group('figure')

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53     def draw_wrapper(artist, renderer, *args, **kwargs):
     54         before(artist, renderer)
---> 55         draw(artist, renderer, *args, **kwargs)
     56         after(artist, renderer)
     57 

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/axes.py in draw(self, renderer, inframe)
   1981 
   1982         for zorder, a in dsu:
-> 1983             a.draw(renderer)
   1984 
   1985         renderer.close_group('axes')

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     53     def draw_wrapper(artist, renderer, *args, **kwargs):
     54         before(artist, renderer)
---> 55         draw(artist, renderer, *args, **kwargs)
     56         after(artist, renderer)
     57 

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/image.py in draw(self, renderer, *args, **kwargs)
    353                 warnings.warn("Image will not be shown correctly with this backend.")
    354 
--> 355             im = self.make_image(renderer.get_image_magnification())
    356             if im is None:
    357                 return

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/image.py in make_image(self, magnification)
    573         im, xmin, ymin, dxintv, dyintv, sx, sy = \
    574             self._get_unsampled_image(self._A, [_x1, _x2, _y1, _y2],
--> 575                                       transformed_viewLim)
    576 
    577         fc = self.axes.patch.get_facecolor()

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/image.py in _get_unsampled_image(self, A, image_extents, viewlim)
    200             else:
    201                 if self._rgbacache is None:
--> 202                     x = self.to_rgba(self._A, self._alpha, bytes=True)
    203                     self._rgbacache = x
    204                 else:

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cm.py in to_rgba(self, x, alpha, bytes)
    211             pass
    212         x = ma.asarray(x)
--> 213         x = self.norm(x)
    214         x = self.cmap(x, alpha=alpha, bytes=bytes)
    215         return x

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py in __call__(self, value, clip)
    843             clip = self.clip
    844 
--> 845         result, is_scalar = self.process_value(value)
    846 
    847         self.autoscale_None(result)

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/colors.py in process_value(value)
    829             if result.dtype.kind == 'f':
    830                 if isinstance(value, np.ndarray):
--> 831                     result = result.copy()
    832             elif result.dtype.itemsize > 2:
    833                 result = result.astype(np.float)

/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in __call__(self, *args, **params)
   2449         mask = instance._mask
   2450         cls = type(instance)
-> 2451         result = getattr(data, methodname)(*args, **params).view(cls)
   2452         result._update_from(instance)
   2453         if result.ndim:

MemoryError: