matplotlib-users

[Matplotlib-users] fill_between and masked array

[Andres L. <and...@ut...>]

Hello,
I try to do fill_between two arrays, that have missing value (masked 
arrays). Following code shows behaviour that seems not correct. Images 
what I expect the result to be (by omitting the missing value) and what 
I get by plotting the whole arrays.

import pylab
import numpy as np
edatmax=np.array([10,4,6,9,np.nan,9,10])
edatmax=np.ma.masked_array(edatmax,np.isnan(edatmax))
edatmin=np.array([8,4,5,1,np.nan,8,5])
edatmin=np.ma.masked_array(edatmin,np.isnan(edatmin))
xtelg=np.arange(edatmax.size)
xtelg=np.ma.masked_array(xtelg,np.isnan(edatmin))
pylab.plot(edatmax,"gx")
pylab.plot(edatmin,"r+")
# comment out to see better
pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3')
# comment in to see better
#pylab.fill_between(xtelg[:4],edatmax[:4],edatmin[:4],facecolor='green',alpha='0.3')
#pylab.fill_between(xtelg[5:],edatmax[5:],edatmin[5:],facecolor='green',alpha='0.3')
pylab.show()

Version of matplotlib is current cvs.

Best regards,
Andres

Re: [Matplotlib-users] fill_between and masked array

[John H. <jd...@gm...>]

On Wed, Apr 29, 2009 at 6:40 AM, Andres Luhamaa <and...@ut...>wrote:

> Hello,
> I try to do fill_between two arrays, that have missing value (masked
> arrays). Following code shows behaviour that seems not correct. Images what
> I expect the result to be (by omitting the missing value) and what I get by
> plotting the whole arrays.
>
> import pylab
> import numpy as np
> edatmax=np.array([10,4,6,9,np.nan,9,10])
> edatmax=np.ma.masked_array(edatmax,np.isnan(edatmax))
> edatmin=np.array([8,4,5,1,np.nan,8,5])
> edatmin=np.ma.masked_array(edatmin,np.isnan(edatmin))
> xtelg=np.arange(edatmax.size)
> xtelg=np.ma.masked_array(xtelg,np.isnan(edatmin))
> pylab.plot(edatmax,"gx")
> pylab.plot(edatmin,"r+")
> # comment out to see better
> pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3')
> # comment in to see better
>
> #pylab.fill_between(xtelg[:4],edatmax[:4],edatmin[:4],facecolor='green',alpha='0.3')
>
> #pylab.fill_between(xtelg[5:],edatmax[5:],edatmin[5:],facecolor='green',alpha='0.3')
> pylab.show()
>
> Version of matplotlib is current cvs.
>


fill_between does not currently support masked arrays, but I think we could
easily extend it to support the mask using the existing support for the
"where" kwarg.  For now, does this behave like you expect?

  valid = ~(edatmax.mask & edatmax.mask )
  pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3',
where=valid)

JDH

Re: [Matplotlib-users] fill_between and masked array

[John H. <jd...@gm...>]

On Wed, Apr 29, 2009 at 10:54 AM, John Hunter <jd...@gm...> wrote:

>
>
> fill_between does not currently support masked arrays, but I think we could
> easily extend it to support the mask using the existing support for the
> "where" kwarg.  For now, does this behave like you expect?
>
>   valid = ~(edatmax.mask & edatmax.mask )
>   pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3',
> where=valid)
>
>

Oops -- meant

 valid = ~(edatmin.mask & edatmax.mask )

JDH

Re: [Matplotlib-users] fill_between and masked array

[Andres L. <and...@ut...>]

John, that's exactly what I wanted, thanks.

Andres

John Hunter wrote:
>
>
> On Wed, Apr 29, 2009 at 10:54 AM, John Hunter <jd...@gm... 
> <mailto:jd...@gm...>> wrote:
>
>
>
>     fill_between does not currently support masked arrays, but I think
>     we could easily extend it to support the mask using the existing
>     support for the "where" kwarg.  For now, does this behave like you
>     expect?
>
>       valid = ~(edatmax.mask & edatmax.mask )
>      
>     pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3',
>     where=valid)
>      
>
>
> Oops -- meant
>
>  valid = ~(edatmin.mask & edatmax.mask )
>
> JDH
>

Re: [Matplotlib-users] fill_between and masked array

[Michael D. <md...@st...>]

I don't believe fill_between directly supports missing values -- but it 
does have the where parameter for this purpose.

We could also be smarter about how "where" is generated when none is 
provided:

        if where is None:
            where = (~np.ma.getmaskarray(x) & ~np.ma.getmaskarray(y1) &
                     ~np.ma.getmaskarray(y2))

...but I'd like more feedback from the author or users of fill_between 
before committing that change.  (That, and Eric Firing can probably find 
a much more efficient way to do the masked array manipulation... ;)

Mike

Andres Luhamaa wrote:
> Hello,
> I try to do fill_between two arrays, that have missing value (masked 
> arrays). Following code shows behaviour that seems not correct. Images 
> what I expect the result to be (by omitting the missing value) and 
> what I get by plotting the whole arrays.
>
> import pylab
> import numpy as np
> edatmax=np.array([10,4,6,9,np.nan,9,10])
> edatmax=np.ma.masked_array(edatmax,np.isnan(edatmax))
> edatmin=np.array([8,4,5,1,np.nan,8,5])
> edatmin=np.ma.masked_array(edatmin,np.isnan(edatmin))
> xtelg=np.arange(edatmax.size)
> xtelg=np.ma.masked_array(xtelg,np.isnan(edatmin))
> pylab.plot(edatmax,"gx")
> pylab.plot(edatmin,"r+")
> # comment out to see better
> pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3')
> # comment in to see better
> #pylab.fill_between(xtelg[:4],edatmax[:4],edatmin[:4],facecolor='green',alpha='0.3') 
>
> #pylab.fill_between(xtelg[5:],edatmax[5:],edatmin[5:],facecolor='green',alpha='0.3') 
>
> pylab.show()
>
> Version of matplotlib is current cvs.
>
> Best regards,
> Andres
>
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Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Re: [Matplotlib-users] fill_between and masked array

[John H. <jd...@gm...>]

On Wed, Apr 29, 2009 at 10:56 AM, Michael Droettboom <md...@st...>wrote:

> I don't believe fill_between directly supports missing values -- but it
> does have the where parameter for this purpose.
>
> We could also be smarter about how "where" is generated when none is
> provided:
>
>        if where is None:
>            where = (~np.ma.getmaskarray(x) & ~np.ma.getmaskarray(y1) &
>                     ~np.ma.getmaskarray(y2))
>
> ...but I'd like more feedback from the author or users of fill_between
> before committing that change.  (That, and Eric Firing can probably find
> a much more efficient way to do the masked array manipulation... ;)


I'm working on a patch for this now....but I would also like Eric to take a
look when I am done since I am a masked array dummy

JDH

Re: [Matplotlib-users] fill_between and masked array

[John H. <jd...@gm...>]

On Wed, Apr 29, 2009 at 11:03 AM, John Hunter <jd...@gm...> wrote:

>
>> ...but I'd like more feedback from the author or users of fill_between
>> before committing that change.  (That, and Eric Firing can probably find
>> a much more efficient way to do the masked array manipulation... ;)
>
>
> I'm working on a patch for this now....but I would also like Eric to take a
> look when I am done since I am a masked array dummy



Here's the diff I just committed::
Index: lib/matplotlib/axes.py
===================================================================
--- lib/matplotlib/axes.py      (revision 7069)
+++ lib/matplotlib/axes.py      (working copy)
@@ -5832,6 +5832,26 @@
         self._process_unit_info(xdata=x, ydata=y1, kwargs=kwargs)
         self._process_unit_info(ydata=y2)

+        if where is None:
+            where = np.ones(len(x), np.bool)
+        else:
+            where = np.asarray(where)
+
+        maskedx = isinstance(x, np.ma.MaskedArray)
+        maskedy1 = isinstance(y1, np.ma.MaskedArray)
+        maskedy2 = isinstance(y2, np.ma.MaskedArray)
+
+        if (maskedx or maskedy1 or maskedy2):
+            if maskedx:
+                where = where & (~x.mask)
+
+            if maskedy1:
+                where = where & (~y1.mask)
+
+            if maskedy2:
+                where = where & (~y2.mask)
+
+
         # Convert the arrays so we can work with them
         x = np.asarray(self.convert_xunits(x))
         y1 = np.asarray(self.convert_yunits(y1))
@@ -5843,10 +5863,7 @@
         if not cbook.iterable(y2):
             y2 = np.ones_like(x)*y2

-        if where is None:
-            where = np.ones(len(x), np.bool)

-        where = np.asarray(where)
         assert( (len(x)==len(y1)) and (len(x)==len(y2)) and
len(x)==len(where))

         polys = []

Re: [Matplotlib-users] fill_between and masked array

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

John Hunter wrote:
> 
> 
> On Wed, Apr 29, 2009 at 11:03 AM, John Hunter <jd...@gm... 
> <mailto:jd...@gm...>> wrote:
> 
> 
>         ...but I'd like more feedback from the author or users of
>         fill_between
>         before committing that change.  (That, and Eric Firing can
>         probably find
>         a much more efficient way to do the masked array manipulation... ;)
> 
> 
>     I'm working on a patch for this now....but I would also like Eric to
>     take a look when I am done since I am a masked array dummy
> 

John,

The way you did it looked OK; but since I was looking at it, I went 
ahead and did some rearranging and condensation to try to make the whole 
thing (not just the mask handling) read better. I doubt there are any 
significant performance differences, but I did not test that. I also 
added a subplot to the fill_between.py demo to illustrate the mask 
handling.  Then I noticed a flaw in the demo plots, and added a note 
about it.  See revision 7071.

Eric