matplotlib-users

[Matplotlib-users] How can I put a white area in the middle of colorbar showing the masked data?

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

Dear all,

In many cases in geoscience mapping we want to show the some missing values
as some special color in the colorbar. like attached one.

I know there is one method in matplotlib colormap called "set_bad", official
docs says:

Set color to be used for masked values.

But I don't know how to make this work when I call the colorbar method.
Is there anyone who have the some successful experience?

Thanks a lot in advance!

Chao
-- 
***********************************************************************************
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] How can I put a white area in the middle of colorbar showing the masked data?

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

sorry, the attached file may lack surfix type, here is the correct one.

Cheers,

chao


On Sat, Mar 1, 2014 at 8:57 PM, Chao YUE <cha...@gm...> wrote:

> Dear all,
>
> In many cases in geoscience mapping we want to show the some missing values
> as some special color in the colorbar. like attached one.
>
> I know there is one method in matplotlib colormap called "set_bad",
> official
> docs says:
>
> Set color to be used for masked values.
>
> But I don't know how to make this work when I call the colorbar method.
> Is there anyone who have the some successful experience?
>
> Thanks a lot in advance!
>
> Chao
> --
>
> ***********************************************************************************
> 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
>
> ************************************************************************************
>



-- 
***********************************************************************************
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] How can I put a white area in the middle of colorbar showing the masked data?

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

On 2014/03/01 9:57 AM, Chao YUE wrote:
> Dear all,
>
> In many cases in geoscience mapping we want to show the some missing values
> as some special color in the colorbar. like attached one.
>
> I know there is one method in matplotlib colormap called "set_bad", official
> docs says:
>
> Set color to be used for masked values.
>
> But I don't know how to make this work when I call the colorbar method.

It is not a matter of calling the colorbar method, but of setting up the 
colormap used on the color-mapped plot for which the colorbar is made.

The one wrinkle to this is that if you are using contourf, the masked 
regions are not filled at all, so they take on the color of the 
background.  To give them the color you assigned to the colormap with 
set_bad, you need to assign that same color to the background, e.g.

ax.set_axis_bgcolor("#bdb76b")

On re-reading your message, however, I think you are asking something 
else, but it is not clear to me from your example exactly what you are 
trying to do.

The colorbar is strictly for a range or sequence of colors, which can 
include triangle regions for the "over" and "under" values; there is no 
place on the colorbar for a "bad" or "missing" value.  Where would you 
put one?  I don't see any such region on the example colorbar you attached.

Eric



> Is there anyone who have the some successful experience?
>
> Thanks a lot in advance!
>
> Chao
> --
> ***********************************************************************************
> 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
> ************************************************************************************
>
>
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Re: [Matplotlib-users] How can I put a white area in the middle of colorbar showing the masked data?

[ChaoYue <cha...@gm...>]

Hi Eric,

thanks for answering. I updated the attached figure.
The idea is, we want to show the tree cover difference, but to make
the negative and positive values very contrastive, we would like to
assign the values falling in small range of change (in the figure, it's -1
to 1)
as blank (or gray), in order to make the remaining data constrasting
different.


The most correct way might be to design a new colormap with white color
exactly in the middle, however this is very tedious, especially if I want
to try
different colormaps. so the alternative approach would be to set the values
falling in (-1,1) as being masked, so they will be the same as the axes
background color as you mentioned (in our case it's white). My question is,
how can I put this background color (which shows maksed data) in the
colorbar,
by avoiding design a new colormap?


Then I notice in the colormap methos there is one called "set_bad", I guess
this
is for this purpose, as in the case of "set_over" and "set_under", which
will
influence the colors in the colorbar when you later call the colorbar
method.
But is it not like this?

I invented an example like below:

import numpy as np
import matplotlib as mat
import matplotlib.pyplot as plt

data = np.random.random(10000).reshape(100,100) - 0.5
data_masked = np.ma.masked_inside(data,-0.05,0.05)
cmap = mat.cm.jet
cmap.set_bad('0.5')
fig,ax = plt.subplots(1,1)
lev = [-0.5,-0.4,-0.3,-0.2,-0.1,-0.05,0,0.05,0.1,0.2,0.3,0.4,0.5]
cas = ax.contourf(data_masked,levels=lev,cmap=cmap)
plt.colorbar(cas,ticks=lev)

In this example, how can I make the colors between -0.05 to 0.05 as white,
if I don't want to bother write a new colormap.

Thanks a lot for your time, I hope this case could be useful for others as I
am sure it's very widely used in geographic related sciences.


Cheers,

Chao



On Sat, Mar 1, 2014 at 9:16 PM, Eric Firing [via matplotlib] <
ml-...@n5...> wrote:

> On 2014/03/01 9:57 AM, Chao YUE wrote:
>
> > Dear all,
> >
> > In many cases in geoscience mapping we want to show the some missing
> values
> > as some special color in the colorbar. like attached one.
> >
> > I know there is one method in matplotlib colormap called "set_bad",
> official
> > docs says:
> >
> > Set color to be used for masked values.
> >
> > But I don't know how to make this work when I call the colorbar method.
>
> It is not a matter of calling the colorbar method, but of setting up the
> colormap used on the color-mapped plot for which the colorbar is made.
>
> The one wrinkle to this is that if you are using contourf, the masked
> regions are not filled at all, so they take on the color of the
> background.  To give them the color you assigned to the colormap with
> set_bad, you need to assign that same color to the background, e.g.
>
> ax.set_axis_bgcolor("#bdb76b")
>
> On re-reading your message, however, I think you are asking something
> else, but it is not clear to me from your example exactly what you are
> trying to do.
>
> The colorbar is strictly for a range or sequence of colors, which can
> include triangle regions for the "over" and "under" values; there is no
> place on the colorbar for a "bad" or "missing" value.  Where would you
> put one?  I don't see any such region on the example colorbar you
> attached.
>
> Eric
>
>
>
> > Is there anyone who have the some successful experience?
> >
> > Thanks a lot in advance!
> >
> > Chao
> > --
> >
> ***********************************************************************************
>
> > 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
> >
> ************************************************************************************
>
> >
> >
> >
> ------------------------------------------------------------------------------
>
> > Flow-based real-time traffic analytics software. Cisco certified tool.
> > Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> > Customize your own dashboards, set traffic alerts and generate reports.
> > Network behavioral analysis & security monitoring. All-in-one tool.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> >
> >
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > [hidden email] <http://user/SendEmail.jtp?type=node&node=42950&i=0>
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
>
>
> ------------------------------------------------------------------------------
>
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> [hidden email] <http://user/SendEmail.jtp?type=node&node=42950&i=1>
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-- 
***********************************************************************************
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
************************************************************************************


colorbar_eg.png (74K) <http://matplotlib.1069221.n5.nabble.com/attachment/42951/0/colorbar_eg.png>




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View this message in context: http://matplotlib.1069221.n5.nabble.com/How-can-I-put-a-white-area-in-the-middle-of-colorbar-showing-the-masked-data-tp42948p42951.html
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Re: [Matplotlib-users] How can I put a white area in the middle of colorbar showing the masked data?

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

On 2014/03/01 11:03 AM, ChaoYue wrote:
> The most correct way might be to design a new colormap with white color
> exactly in the middle, however this is very tedious, especially if I
> want to try
> different colormaps. so the alternative approach would be to set the values
> falling in (-1,1) as being masked, so they will be the same as the axes
> background color as you mentioned (in our case it's white). My question is,
> how can I put this background color (which shows maksed data) in the
> colorbar,
> by avoiding design a new colormap?

It's not the answer you want to hear, but I think the correct answer is 
that you should do this via the colormap, and not by masking the low 
values.  It doesn't have to be painful.  If, in contourf, you use a 
diverging colormap with white already in the middle 
(http://matplotlib.org/examples/color/colormaps_reference.html) and a 
norm with symmetric limits (vmin and vmax; you can let them be set 
automatically after you specify your symmetric set of contour boundaries 
appropriately) then it will be done for you.

e.g.,

z = 10 * np.random.randn(20, 30)
clevs = [-10, -5, -2, -1, 1, 2, 5, 10]
cs = plt.contourf(z, levels=clevs, cmap=plt.get_cmap('PRGn'),
                   extend='both')
cbar = plt.colorbar(cs, spacing='uniform')

Eric

Re: [Matplotlib-users] How can I put a white area in the middle of colorbar showing the masked data?

[ChaoYue <cha...@gm...>]

Dear Eric,

This solved part of my problem. thanks a lot.
I think I will revisit this issue when I have time (not promised).
do you think this could be some feature desirable?

Cheers,

Chao


On Sat, Mar 1, 2014 at 10:39 PM, Eric Firing [via matplotlib] <
ml-...@n5...> wrote:

> On 2014/03/01 11:03 AM, ChaoYue wrote:
> > The most correct way might be to design a new colormap with white color
> > exactly in the middle, however this is very tedious, especially if I
> > want to try
> > different colormaps. so the alternative approach would be to set the
> values
> > falling in (-1,1) as being masked, so they will be the same as the axes
> > background color as you mentioned (in our case it's white). My question
> is,
> > how can I put this background color (which shows maksed data) in the
> > colorbar,
> > by avoiding design a new colormap?
>
> It's not the answer you want to hear, but I think the correct answer is
> that you should do this via the colormap, and not by masking the low
> values.  It doesn't have to be painful.  If, in contourf, you use a
> diverging colormap with white already in the middle
> (http://matplotlib.org/examples/color/colormaps_reference.html) and a
> norm with symmetric limits (vmin and vmax; you can let them be set
> automatically after you specify your symmetric set of contour boundaries
> appropriately) then it will be done for you.
>
> e.g.,
>
> z = 10 * np.random.randn(20, 30)
> clevs = [-10, -5, -2, -1, 1, 2, 5, 10]
> cs = plt.contourf(z, levels=clevs, cmap=plt.get_cmap('PRGn'),
>                    extend='both')
> cbar = plt.colorbar(cs, spacing='uniform')
>
> Eric
>
> ------------------------------------------------------------------------------
>
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> [hidden email] <http://user/SendEmail.jtp?type=node&node=42952&i=0>
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
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>  If you reply to this email, your message will be added to the discussion
> below:
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>  To start a new topic under matplotlib - users, email
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-- 
***********************************************************************************
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
************************************************************************************




--
View this message in context: http://matplotlib.1069221.n5.nabble.com/How-can-I-put-a-white-area-in-the-middle-of-colorbar-showing-the-masked-data-tp42948p42956.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Re: [Matplotlib-users] How can I put a white area in the middle of colorbar showing the masked data?

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

On 2014/03/02 1:02 AM, ChaoYue wrote:
> Dear Eric,
>
> This solved part of my problem. thanks a lot.
> I think I will revisit this issue when I have time (not promised).
> do you think this could be some feature desirable?

I don't understand what feature you are referring to; evidently I don't 
understand what the problem is, so I don't know what part remains unsolved.

Eric


>
> Cheers,
>
> Chao
>
>
> On Sat, Mar 1, 2014 at 10:39 PM, Eric Firing [via matplotlib] <[hidden
> email] </user/SendEmail.jtp?type=node&node=42956&i=0>> wrote:
>
>     On 2014/03/01 11:03 AM, ChaoYue wrote:
>      > The most correct way might be to design a new colormap with white
>     color
>      > exactly in the middle, however this is very tedious, especially if I
>      > want to try
>      > different colormaps. so the alternative approach would be to set
>     the values
>      > falling in (-1,1) as being masked, so they will be the same as
>     the axes
>      > background color as you mentioned (in our case it's white). My
>     question is,
>      > how can I put this background color (which shows maksed data) in the
>      > colorbar,
>      > by avoiding design a new colormap?
>
>     It's not the answer you want to hear, but I think the correct answer is
>     that you should do this via the colormap, and not by masking the low
>     values.  It doesn't have to be painful.  If, in contourf, you use a
>     diverging colormap with white already in the middle
>     (http://matplotlib.org/examples/color/colormaps_reference.html) and a
>     norm with symmetric limits (vmin and vmax; you can let them be set
>     automatically after you specify your symmetric set of contour
>     boundaries
>     appropriately) then it will be done for you.
>
>     e.g.,
>
>     z = 10 * np.random.randn(20, 30)
>     clevs = [-10, -5, -2, -1, 1, 2, 5, 10]
>     cs = plt.contourf(z, levels=clevs, cmap=plt.get_cmap('PRGn'),
>                         extend='both')
>     cbar = plt.colorbar(cs, spacing='uniform')
>
>     Eric
>
>     ------------------------------------------------------------------------------

Re: [Matplotlib-users] How can I put a white area in the middle of colorbar showing the masked data?

[Martin M. <mmo...@fo...>]

Maybe I understand what he means. How can a user override some value in a
colormap? Lets say, in general user wants to inherit some ready made colormap
but in addition wants to force certain colors to some data items.
M.

Eric Firing wrote:
> On 2014/03/02 1:02 AM, ChaoYue wrote:
>> Dear Eric,
>>
>> This solved part of my problem. thanks a lot.
>> I think I will revisit this issue when I have time (not promised).
>> do you think this could be some feature desirable?
> 
> I don't understand what feature you are referring to; evidently I don't 
> understand what the problem is, so I don't know what part remains unsolved.
> 
> Eric
> 
> 
>>
>> Cheers,
>>
>> Chao
>>
>>
>> On Sat, Mar 1, 2014 at 10:39 PM, Eric Firing [via matplotlib] <[hidden
>> email] </user/SendEmail.jtp?type=node&node=42956&i=0>> wrote:
>>
>>     On 2014/03/01 11:03 AM, ChaoYue wrote:
>>      > The most correct way might be to design a new colormap with white
>>     color
>>      > exactly in the middle, however this is very tedious, especially if I
>>      > want to try
>>      > different colormaps. so the alternative approach would be to set
>>     the values
>>      > falling in (-1,1) as being masked, so they will be the same as
>>     the axes
>>      > background color as you mentioned (in our case it's white). My
>>     question is,
>>      > how can I put this background color (which shows maksed data) in the
>>      > colorbar,
>>      > by avoiding design a new colormap?
>>
>>     It's not the answer you want to hear, but I think the correct answer is
>>     that you should do this via the colormap, and not by masking the low
>>     values.  It doesn't have to be painful.  If, in contourf, you use a
>>     diverging colormap with white already in the middle
>>     (http://matplotlib.org/examples/color/colormaps_reference.html) and a
>>     norm with symmetric limits (vmin and vmax; you can let them be set
>>     automatically after you specify your symmetric set of contour
>>     boundaries
>>     appropriately) then it will be done for you.
>>
>>     e.g.,
>>
>>     z = 10 * np.random.randn(20, 30)
>>     clevs = [-10, -5, -2, -1, 1, 2, 5, 10]
>>     cs = plt.contourf(z, levels=clevs, cmap=plt.get_cmap('PRGn'),
>>                         extend='both')
>>     cbar = plt.colorbar(cs, spacing='uniform')
>>
>>     Eric
>>
>>     ------------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>