matplotlib-users — Discussion related to using matplotlib

[Matplotlib-users] filled contours, and missing data

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

John et al.,

I would like to phase in matplotlib to replace Matlab ASAP for plotting 
physical oceanographic observations, primarily current profile 
measurements.  I (and many other physical oceanographers) primarily use 
contourf to plot filled contours; I only rarely use line contours.  It 
looks to me like gcntr.c has the necessary functionality--the ability to 
output polygons enclosing regions between a pair of specified levels. 
Is someone already working on exposing that functionality in matplotlib, 
or is it planned?

It appears that gcntr.c also has the ability to handle missing data via 
setting elements of the reg array to zero, and that this could be 
exposed fairly easily in the contour method in axes.py by adding "reg" 
to the set of kwargs.  Correct?  If so, is this also planned?

The question of missing data handling in contour plotting brings up the 
more general issue of how to handle data gaps in plots.  For example, 
the ocean current profiles that I measure using a Doppler profiler 
extend to varying depths, and sometimes have holes in the middle where 
there are not enough acoustic scatterers to give a signal.  This sort of 
thing--data gaps--is universal in physical oceanography.  One of 
Matlab's major strengths is the way it handles them, using nan as a bad 
value flag.  Plotting a line with the plot command, the line is broken 
at each nan; so if there is a hole in the data, the plot shows exactly 
that.  The same for contouring: nans are automatically used as a mask.

Obviously, not everyone needs this kind of automatic handling of data 
gaps, but I think it would be very useful for many applications, so I 
hope it can be considered as a possible goal.  At the plotting level, 
collections may make it easier to implement than would have been the 
case in the early days of matplotlib.  At the array manipulation level, 
the implementation could involve either masked arrays or nans.  I would 
greatly prefer the Matlab-style nan approach, but I don't know whether 
this would work with Numeric.  Maybe in Numeric3?  Numarray appears 
better equipped, with its ieeespecial.py module.

Thanks for the enormous amount of beautiful work you have already done!

Eric

Re: [Matplotlib-users] axes.autoscale_view

[John H. <jdh...@ac...>]

>>>>> "Malte" == Malte Marquarding <Mal...@cs...> writes:

    Malte> Hi, is it possible to only autoscale on one axis.  I'd like
    Malte> to set the xlimits but have the ylimits autoscaled.

Any problem with?

  plot(something)  # y and y are autoscaled
  xlim(0,2)        # set your own xlim

JDH

Re: [Matplotlib-users] updating matshow

[John H. <jdh...@ac...>]

>>>>> "Darren" == Darren Dale <dd...@co...> writes:

    Darren> I like the new matshow function. Is it possible to update
    Darren> the data? I was looking for the equivalent of an imshow
    Darren> object's set_data method, but it is not exposed to
    Darren> matshow.

matshow returns the image object, so you should be able to call
set_data on this instance.  Of course, the new array needs to have the
same aspect ratio as the original if you want the aspect preserving
features of matshow.

    Darren> This is a nice function for plotting microscopy images,
    Darren> since the aspect ratio is fixed. Is there any object to
    Darren> allowing the origin kwarg to do reorient the origin of the
    Darren> image?  --

I don't think so.  Take a look at the implementation of matshow in
pylab.py.  It is broken into two pieces.  The hard part is being done
in matplotlib.figure.figaspect, which creates the figure with the
right aspect ratio -- as long as you create an axes with equal width
and height, your axes will have the right aspect too.

You can use this figaspect yourself, and then simply call imshow with
the args you want.

  from matplotlib.figure import figaspect
  w,h = figaspect(arr)
  fig = figure(figsize=(w,h))
  ax  = fig.add_axes([0.15, 0.09, 0.775, 0.775])
  ax.imshow(arr, origin='upper', interpolation='nearest')

JDH

[Matplotlib-users] Re: [IPython-user] crash report

[John H. <jdh...@ac...>]

>>>>> "Darren" == Darren Dale <dd...@co...> writes:


    Darren> I am using ipython -pylab, and can reproduce this error
    Darren> with the following unusual steps:

Thanks Darren,

I think the easiest thing to do here is raise on the call to
set_position if w==0 or h ==0

JDH

[Matplotlib-users] crash report

[Darren D. <dd...@co...>]

I am using ipython -pylab, and can reproduce this error with the following 
unusual steps:

a=rand(500,500)
figimage(a)
ax=gca()
ax.set_position([0,1,0,1]) # this is should be [0,0,1,1]
draw()
# traceback here, thats expected...
# fix my mistake
ax.set_position([0,0,1,1])
# now moving the mouse pointer over the image causes the crash report to be 
generated.

The first call to set_position I got the order confused with imshow's extent, 
which is [xmin,xmax,ymin,ymax] instead of the usual [xmin,ymin,dx,dy]. Like I 
said, its a bizarre set of circumstances, but I thought I should report it.

-- 

Darren

[Matplotlib-users] updating matshow

[Darren D. <dd...@co...>]

I like the new matshow function. Is it possible to update the data? I was 
looking for the equivalent of an imshow object's set_data method, but it is 
not exposed to matshow.

This is a nice function for plotting microscopy images, since the aspect ratio 
is fixed. Is there any object to allowing the origin kwarg to do reorient the 
origin of the image?
-- 

Darren

[Matplotlib-users] axes.autoscale_view

[Malte M. <Mal...@cs...>]

Hi,

is it possible to only autoscale on one axis.
I'd like to set the xlimits but have the ylimits autoscaled.

Cheers,
Malte.

Re: [Matplotlib-users] Event blocking

[Malte M. <Mal...@cs...>]

If one reads the docs (Goals) one finds the answer
"Yet to be added is a blocking function, like x, y = mouse_press(*args) "


Cheers,
Malte.

[Matplotlib-users] linestyles in contour?

[James B. <bo...@ll...>]

 From what I can gather, I can change the line colors and widths in the 
contour routine but cannot specify a line style
such as dashed, dotted etc.

Is this true? If so I would like to have this capability - it makes 
black and white plots easier to interpret.

In any case the contour in 0.72 works great - thanks

--JIm

Re: [Matplotlib-users] Getting the size of Text objects

[John H. <jdh...@ac...>]

>>>>> "Chris" == Chris Barker <Chr...@no...> writes:

    Chris> Hi all, Is there a way to get the size of a text object? I
    Chris> can't seem to find a method that does that. The
    Chris> functionality must be in there somewhere, or having
    Chris> different reference points wouldn't work.

The size of a text object is tricky.  Do you mean the width and height
in points?  Or in data coords?  The x,y location of text is in one
coordinate system (axes, figure or data), but the width and height are
not.  To convert between coordinate systems (eg points or display
versus data) the way mpl does it is to one transform coord system to
display and use the other coordinate system to inverse transform.
This would enable you to get, for example, a text bounding box in data
coords, but could be screwed up by a figure resize.

If you tell me more precisely what you are trying to achieve, I might
be able to help you or think about design changes to accommodate it.
FYI, this is an issue that crops up a lot and is vexing.  What one
would like to be able to do is use a layout engine and say, place
object one above and to the right of object 2 with a pad of 2 points.

The text instance can give you its bounding box in display if you pass
it the backend renderer -- this is required because the width and
height can be backend dependent.  I suppose you are using OO agg based
on your previous posts.  One problem with the current design that is
that the agg canvas doesn't generate it's renderer until draw time
(with caching), but you need access to the renderer before draw time
for layout that depends on text.  If we move this logic to a
get_renderer method, you can use it at draw time.  I'll attach a
replacement backend_agg.FigureCanvasAgg class to support this below

    from matplotlib.figure import Figure
    from matplotlib.backends.backend_agg import FigureCanvasAgg

    fig = Figure()
    canvas = FigureCanvasAgg(fig)
    renderer = canvas.get_renderer()
    ax = fig.add_subplot(111)
    ax.plot([1,2,3])
    t = ax.text(1,2,'hi mom')
    bbox =  t.get_window_extent(renderer)
    print 'display', bbox.get_bounds()  #l,b,w,h

    # get the axes data coords bbox of this display bounding box
    from matplotlib.transforms import inverse_transform_bbox
    axbox = inverse_transform_bbox(ax.transData, bbox)

    print 'data coords', axbox.get_bounds()

    fig.savefig('test')




In backend_agg.py FigureCanvasAgg, replace the draw method with the following 2
methods

    def draw(self):
        """
        Draw the figure using the renderer
        """
        if __debug__: verbose.report('FigureCanvasAgg.draw', 'debug-annoying')

        renderer = self.get_renderer()
        self.figure.draw(renderer)

    def get_renderer(self):
        l,b,w,h = self.figure.bbox.get_bounds()
        key = w, h, self.figure.dpi.get()
        try: self._lastKey, self.renderer
        except AttributeError: need_new_renderer = True
        else:  need_new_renderer = (self._lastKey != key)

        if need_new_renderer:
            self.renderer = RendererAgg(w, h, self.figure.dpi)
            self._lastKey = key
        return self.renderer


Hope this gets you started -- if you provide more details we maybe
able to improve from here.

JDG

[Matplotlib-users] Getting the size of Text objects

[Chris B. <Chr...@no...>]

Hi all,

Is there a way to get the size of a text object? I can't seem to find a 
method that does that. The functionality must be in there somewhere, or 
having different reference points wouldn't work.

-thanks, Chris



-- 
Christopher Barker, Ph.D.
Oceanographer
                                     		
NOAA/OR&R/HAZMAT         (206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

Re: [Matplotlib-users] Saving (and loading) binary data with matrix shape and type storage

[Chris B. <Chr...@no...>]

OOPS, forgot the enclosure.

-Chris

-- 
Christopher Barker, Ph.D.
Oceanographer
                                     		
NOAA/OR&R/HAZMAT         (206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

Re: [Matplotlib-users] Saving (and loading) binary data with matrix shape and type storage

[Chris B. <Chr...@no...>]

Xavier Gnata wrote:
> Hi,
> 
> How can I save (and relaod) a matrix into a binary file *with* matrix 
> shape and type storage.
> I have a feature request :
> Basically, it would be great to be able to do something like :
> 
> X  = rand(100,100)
> BSave('foo.dat', X)
> Y =  BLoad('foo.dat')

I don't know of an existing function that does this, but it would not be 
hard to roll your own. All you need to do is first write the dimensions 
and type of the array to the file, then the binary data. To read it back 
in, you'd first read in the meta data, then the binary data, and you're 
done.

I've enclosed a quickie prototype (using Numeric, I think numarray may 
have tofile() and fromfile() methods, and it handles typecode differently.

By the way, there may be something in SciPy for this, and it's also 
possible that arrays can be pickled.

This is also a better question for the NumPy list than this list.

-Chris





-- 
Christopher Barker, Ph.D.
Oceanographer
                                     		
NOAA/OR&R/HAZMAT         (206) 526-6959   voice
7600 Sand Point Way NE   (206) 526-6329   fax
Seattle, WA  98115       (206) 526-6317   main reception

Chr...@no...

Re: [Matplotlib-users] bug in autoscale

[John H. <jdh...@ac...>]

>>>>> "Humufr" == Humufr  <hu...@ya...> writes:
    Humufr> matplotlib CVS version.

There was a bug in the autoscaler in CVS briefly before the 0.72
release, but this was fixed.  I reformatted your example into python
code and it runs fine with current CVS.  

I appreciate the report, but could I ask you to do 2 things next time?
Please send proper python code which exposes the the bug (eg your
lists are not python lists) and report either the matplotlib version
that exposes the bug, or if you are using CVS, the revision number.

For example, if you suspect a bug in the ticking (where the autoscaler
lives)

> cvs status lib/matplotlib/ticker.py

===================================================================
File: ticker.py         Status: Up-to-date
 
   Working revision:    1.14
   Repository revision: 1.14    /cvsroot/matplotlib/matplotlib/lib/matplotlib/ticker.py,v

There is a problem with sourceforge that non-developer CVS checkouts
have long lags (eg the CVS version you get may be older than the
latest release!) but sourceforge says they are trying to fix this.

Thanks!
JDH

Re: [Matplotlib-users] figimage filling entire image

[John H. <jdh...@ac...>]

>>>>> "Rich" == Rich Drewes <dr...@in...> writes:


    Rich> Thanks for your response.  I am familiar with implot however
    Rich> I've never been able to get it to plot with distinct pixel
    Rich> boundaries.  What I want is a figimage-like plot with
    Rich> distinct, single-color regions, just larger regions, so that
    Rich> the entire screen window is filled.  No smoothing or
    Rich> interpolation, just big chunky pixels.

Hi Rich,

You'll probably want to use

  imshow(X, interpolation='nearest')

to prevent smoothing / interpolation.

    Rich> "you can define an Axes with size [0,1,0,1]"

    Rich> The order of the points is wrong there, and you set me
    Rich> straight.

OK, I'll fix that for the next release, thanks.

See also the matshow command new to 0.72 which created an axes with
the same aspect ration as your array.

JDH

Re: [Matplotlib-users] Markers in legend?

[Robert L. <ro...@le...>]

John Hunter wrote:
>     Robert> Is it possible to include a marker from one or more
>     Robert> scatter plots in the legend?
> 
> This is a bit tricky -- scatter plots can vary in size and color.

Well, in my newbie-ness I wasn't aware that this was the case.

> What should one use for the legend marker?  So the short answer is no.
> My question for you is, "how *should* it work?"
> 
> Not if you are using homogeneous marker sizes and colors, I suggest
> using plot markers tweaking the properties, as in
> 
>   line, = plot(x,y,linestyle='None', marker='s', 
>                markerfacecolor='red', markeredgecolor='g',
>                markersize=20, markeredgewith=3)
> 

For me, this is exactly how it should work - thanks!

Robert

[Matplotlib-users] Event blocking

[Malte M. <Mal...@cs...>]

Hi,

I remember reading quite a while ago that event blocking  (request/reply) was 
on the list of todos.

Is it possible to wait for an event to be fired, i.e. having a function 
request an event and return when it has been emitted.

All examples only show "GUI" actions on events.


Cheers,
Malte.

[Matplotlib-users] bug in autoscale

[Humufr <hu...@ya...>]

with:

test = [ 32.539772  32.504516  32.47944   32.380905  32.31546   32.193687
  32.20433   32.008384  32.081062  32.065277  31.934586  32.09236
  31.952614  32.146781  31.724289  31.52745   31.535683  31.596657
  31.543633  31.562935  31.882072  31.717575  31.675995  31.609718
  31.52964   31.4748    31.325775  31.239838  31.350319  31.172882
  31.58982   31.549728  31.277122  31.196587  31.15017   30.995155
  30.917984  31.02172   30.932365  31.364365  31.20729   30.92582 ]

toto = [ 4781.7     4813.9     4846.1     4878.3     4910.5
4942.7     4974.9
  5007.1     5039.3     5071.5     5103.7     5135.9     5168.1     5200.3
  5232.5     5264.7     5296.9     5329.1     5361.3     5393.5     5425.7
  5457.9     5490.1     5522.3002  5554.5     5586.7     5618.9     5651.1
  5683.3002  5715.5     5747.7     5779.9     5812.1     5844.3002
  5860.4     5876.5     5908.7     5940.9     5973.1     6005.3002
  6037.5     6069.7   ]

max(test) = 36.347007

plot (toto,test)

I obtain axes between:

x= [4600,6200]
y= [0,5000]


matplotlib CVS version.

Re: [Matplotlib-users] figimage filling entire image

[Rich D. <dr...@in...>]

On Thu, 17 Feb 2005, Perry Greenfield wrote:

> Sure. To fill the entire window:
> 
> axes((0,0,1,1)) # defines the axes bound to use the whole figure region 

Yes!  There is (I think) an error in the documentation, both HTML online
(http://matplotlib.sourceforge.net/matplotlib.pylab.html#-figimage) and
also the .pdf version, where it says this:

"you can define an Axes with size [0,1,0,1]"

The order of the points is wrong there, and you set me straight.

Thanks much,
Rich

Re: [Matplotlib-users] figimage filling entire image

[Perry G. <pe...@st...>]

On Feb 17, 2005, at 10:22 AM, Rich Drewes wrote:

> On Thu, 17 Feb 2005, Perry Greenfield wrote:
>
>> If you want an image to spatially scale with the plot window, use
>> implot instead of figimage. Figimage does not resample images 
>> spatially
>> but rather displays them pixel for pixel (that's what distinguishes
>> the two functions)
>
> Thanks for your response.  I am familiar with implot however I've never
> been able to get it to plot with distinct pixel boundaries.  What I 
> want
> is a figimage-like plot with distinct, single-color regions, just 
> larger
> regions, so that the entire screen window is filled.  No smoothing or
> interpolation, just big chunky pixels.
>
> Can this be done?
>
> Rich

Sure. To fill the entire window:

axes((0,0,1,1)) # defines the axes bound to use the whole figure region 
(i.e, window)
imshow(imdata, interpolation="nearest") # use nearest neighbor 
interpolation to rescale image

Is this what you are looking for?

Perry

RE: [Matplotlib-users] figimage filling entire image

[Rich D. <dr...@in...>]

On Thu, 17 Feb 2005, Perry Greenfield wrote:

> If you want an image to spatially scale with the plot window, use 
> implot instead of figimage. Figimage does not resample images spatially
> but rather displays them pixel for pixel (that's what distinguishes 
> the two functions)

Thanks for your response.  I am familiar with implot however I've never
been able to get it to plot with distinct pixel boundaries.  What I want
is a figimage-like plot with distinct, single-color regions, just larger
regions, so that the entire screen window is filled.  No smoothing or
interpolation, just big chunky pixels.

Can this be done?

Rich

[Matplotlib-users] Trans.: Matplotlib-users -- confirmation of subscription -- request 484335

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[Matplotlib-users] problem : installation of matplotlib under zope

[fabian s. <fs...@ce...>]

I develop a web application  under  zope and I would like installing  
matplotlib under zope.Considering that the python of zope has no the 
entry in the register, how installing matplotlib?
thanks

[Matplotlib-users] Saving (and loading) binary data with matrix shape and type storage

[Xavier G. <gn...@ob...>]

Hi,

How can I save (and relaod) a matrix into a binary file *with* matrix 
shape and type storage.
I have a feature request :
Basically, it would be great to be able to do something like :

X  = rand(100,100)
BSave('foo.dat', X)
Y =  BLoad('foo.dat')

and at this point, we sould have X==Y (without having to use reshape and 
having to take care on types)

Waiting for such a feature, I'm using gzipped ASCII files but IMHO it is 
far to be the best solution.

Cheers.
Xavier.
ps : Everything else seems to work just great in 0.72 : Thank's for all 
the job on matplotlib.

RE: [Matplotlib-users] figimage filling entire image

[Perry G. <pe...@st...>]

If you want an image to spatially scale with the plot window, use 
implot instead of figimage. Figimage does not resample images spatially
but rather displays them pixel for pixel (that's what distinguishes 
the two functions)

Perry Greenfield

> -----Original Message-----
> From: mat...@li...
> [mailto:mat...@li...]On Behalf Of Rich
> Drewes
> Sent: Wednesday, February 16, 2005 11:24 PM
> To: mat...@li...
> Subject: [Matplotlib-users] figimage filling entire image
> 
> 
> Hello,
> 
> I'm trying to get a figimage to be scaled up dimensionally to occupy the 
> entire plot window rather than scrunched up in the upper left.  The docs 
> cryptically suggest:
> 
> " * origin is either 'upper' or 'lower', which indicates where the [0,0]
>     index of the array is in the upper left or lower left corner of
>     the axes.  Defaults to the rc image.origin value
>  
> This complements the axes image which will be resampled to fit the
> current axes.  If you want a resampled image to fill the entire
> figure, you can define an Axes with size [0,1,0,1]."
> 
> But that is too cryptic for my current knowledge state.  The following
> creates a scrunched image:
> 
> figure(1)
> d=rand(100, 100)
> figimage(d)
> show()
> 
> But this, probably naive guess, errors out with a 
> transformation-not-invertible message:
> 
> figure(1)
> axes([0,1,0,1])
> d=rand(100, 100)
> figimage(d)
> show()
> 
> Suggestions appreciated.  Thanks,
> 
> Rich
> 
> 
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