matplotlib-users

[Matplotlib-users] color missing value with contourf

[Francesco B. <fra...@bs...>]

Hi all,

I'm using pygrads for plotting maps from netcdf files.

I use the contourf method, but I'm not able to fill the region where there are
no value (there is the missing value -999) with a color. It seems to ignore
the set_bad method that I used to make the colormap.

Any suggestions?

Thank you very much in advance.

-- 
| Francesco Benincasa

Re: [Matplotlib-users] color missing value with contourf

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

On Tue, Feb 1, 2011 at 11:09 AM, Francesco Benincasa <
fra...@bs...> wrote:

> Hi all,
>
> I'm using pygrads for plotting maps from netcdf files.
>
> I use the contourf method, but I'm not able to fill the region where there
> are
> no value (there is the missing value -999) with a color. It seems to ignore
> the set_bad method that I used to make the colormap.
>
> Any suggestions?
>
> Thank you very much in advance.
>
> --
> | Francesco Benincasa
>
>
Most likely, the issue is that set_bad is more for setting the color when
encountering masked values (through masked arrays).  As a quick and dirty
way to deal with it, try setting that color through the set_under() method.

The correct way to do this is to use set_bad, but convert  your numpy array
that you are displaying into a masked array like so:

z_ma = np.ma.masked_array(z, mask=(z == -999))

and use contourf on z_ma.

Let us know how that works for you.

Ben Root

Re: [Matplotlib-users] color missing value with contourf

[Mahe <mah...@gm...>]

Benjamin Root <ben.root@...> writes:

> 
> On Tue, Feb 1, 2011 at 11:09 AM, Francesco Benincasa <francesco.benincasa-
DuY...@pu...> wrote:
> 
> Hi all,
> I'm using pygrads for plotting maps from netcdf files.
> I use the contourf method, but I'm not able to fill the region where there are
> no value (there is the missing value -999) with a color. It seems to ignore
> the set_bad method that I used to make the colormap.
> Any suggestions?
> Thank you very much in advance.
> --
> | Francesco Benincasa
> 
> 
> Most likely, the issue is that set_bad is more for setting the color when 
encountering masked values (through masked arrays).  As a quick and dirty way to 
deal with it, try setting that color through the set_under() method.The correct 
way to do this is to use set_bad, but convert  your numpy array that you are 
displaying into a masked array like so:z_ma = np.ma.masked_array(z, mask=(z == 
-999))and use contourf on z_ma.Let us know how that works for you.Ben Root
> 
> 
> 
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> 

Hi !
I have had the same issue (set_bad not taking effect with nans), and transformed 
the data into a masked array. But it does not seem to work...
Here a minimal example:

import matplotlib.pyplot as plt
import numpy as np

plt.clf()
x = np.linspace(-180,180,100)
y = np.linspace(-90,90,100)
x, y = np.meshgrid(x,y)
data = np.cos(x/180*np.pi) + np.sin(y/180*np.pi)
data[(y<50)&(y>30)&(x<50)&(x>30)] = np.nan
data = np.ma.masked_array(data, mask = np.isnan(data)) # has no effect
ncol = 20
cbar = [-1,1]
palette = plt.cm.Blues
palette.set_bad('green')
palette.set_over('red')
palette.set_under('black')
cs = plt.contourf(x,y,data,np.linspace(cbar[0],cbar[1],ncol), cmap=palette, 
extend='both')
plt.colorbar()
cs.set_clim(cbar) # need that for set_upper and set_lower to take effect
plt.show()

There is already that small bug where one needs to call set_clim for set_upper 
and set_lower, maybe something similar is needed for set_bad?
Any idea?

Many thanks,
Mahe

Re: [Matplotlib-users] color missing value with contourf

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

On Tue, Mar 5, 2013 at 5:33 PM, Mahe <mah...@gm...> wrote:

>
> Benjamin Root <ben.root@...> writes:
>
> >
> > On Tue, Feb 1, 2011 at 11:09 AM, Francesco Benincasa
> <francesco.benincasa-
> DuY...@pu...> wrote:
> >
> > Hi all,
> > I'm using pygrads for plotting maps from netcdf files.
> > I use the contourf method, but I'm not able to fill the region where
> there are
> > no value (there is the missing value -999) with a color. It seems to
> ignore
> > the set_bad method that I used to make the colormap.
> > Any suggestions?
> > Thank you very much in advance.
> > --
> > | Francesco Benincasa
> >
> >
> > Most likely, the issue is that set_bad is more for setting the color when
> encountering masked values (through masked arrays).  As a quick and dirty
> way to
> deal with it, try setting that color through the set_under() method.The
> correct
> way to do this is to use set_bad, but convert  your numpy array that you
> are
> displaying into a masked array like so:z_ma = np.ma.masked_array(z,
> mask=(z ==
> -999))and use contourf on z_ma.Let us know how that works for you.Ben Root
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> > Finally, a world-class log management solution at an even better
> price-free!
> > Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> > February 28th, so secure your free ArcSight Logger TODAY!
> > http://p.sf.net/sfu/arcsight-sfd2d
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Matplotlib-users@...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
>
> Hi !
> I have had the same issue (set_bad not taking effect with nans), and
> transformed
> the data into a masked array. But it does not seem to work...
> Here a minimal example:
>
> import matplotlib.pyplot as plt
> import numpy as np
>
> plt.clf()
> x = np.linspace(-180,180,100)
> y = np.linspace(-90,90,100)
> x, y = np.meshgrid(x,y)
> data = np.cos(x/180*np.pi) + np.sin(y/180*np.pi)
> data[(y<50)&(y>30)&(x<50)&(x>30)] = np.nan
> data = np.ma.masked_array(data, mask = np.isnan(data)) # has no effect
> ncol = 20
> cbar = [-1,1]
> palette = plt.cm.Blues
> palette.set_bad('green')
> palette.set_over('red')
> palette.set_under('black')
> cs = plt.contourf(x,y,data,np.linspace(cbar[0],cbar[1],ncol), cmap=palette,
> extend='both')
> plt.colorbar()
> cs.set_clim(cbar) # need that for set_upper and set_lower to take effect
> plt.show()
>
> There is already that small bug where one needs to call set_clim for
> set_upper
> and set_lower, maybe something similar is needed for set_bad?
> Any idea?
>
> Many thanks,
> Mahe
>
>
Your problem is very, very subtle, and we probably should handle this
better.  The issue is, I think, that because of the way contourf works, the
colormap is applied to the list of polygon (or patch) collections, each
having a value for its level.  Because there wouldn't be a "nan" level,
there is no polygon or patch at all for that spot.  Indeed, if you change
the background color of the plot, the white patch becomes whatever color
the background is.

I hope this clears it up for you.

Ben Root