Replace NaN in 32-bit images with 0

[mjlm]

Hi there,

Is there a simple way to "reset" all pixels with the value "NaN" to a specified numeric value, e.g. 0?

I couldn't find a way to do this properly in ImageJ...one ugly workaround I came up with is to save the image as text and then simply find & replace all occurences of NaN, but that's not a feasible option for large stacks...there MUST be a better way.

Thanks!

[Michael Schmid]

Hi anonymous,

this may look stupid, but it works at least with the NaN created by  
division by zero:
Enter in the Process>Math>Macro
     if (!(v<1) && !(v>0)) v=0;

A NaN value fulfills no inequality; all 'true' numbers are either <1  
or >0 or both.
Of course, a macro function 'isNaN(value)' would be nice to have...

Michael
________________________________________________________________

On 23 Mar 2011, at 18:03, mjlm wrote:

> Hi there,
>
> Is there a simple way to "reset" all pixels with the value "NaN" to a
> specified numeric value, e.g. 0?
>
> I couldn't find a way to do this properly in ImageJ...one ugly  
> workaround I
> came up with is to save the image as text and then simply find &  
> replace all
> occurences of NaN, but that's not a feasible option for large  
> stacks...there
> MUST be a better way.
>
> Thanks!

[ctrueden]

Hi Michael & anonymous,

Can't you simply write "if (v != v) v = 0;" since NaN is not even equal to
itself?

It's funny—in older versions of Java, the "v != v" test was much faster than
"Double.isNaN(v)" due to the overhead of method calls, but the JIT has since
overcome this problem.

-Curtis

On Wed, Mar 23, 2011 at 12:40 PM, Michael Schmid <[hidden email]>wrote:

> Hi anonymous,
>
> this may look stupid, but it works at least with the NaN created by
> division by zero:
> Enter in the Process>Math>Macro
>    if (!(v<1) && !(v>0)) v=0;
>
> A NaN value fulfills no inequality; all 'true' numbers are either <1 or >0
> or both.
> Of course, a macro function 'isNaN(value)' would be nice to have...
>
> Michael
> ________________________________________________________________
>
>
> On 23 Mar 2011, at 18:03, mjlm wrote:
>
>  Hi there,
>>
>> Is there a simple way to "reset" all pixels with the value "NaN" to a
>> specified numeric value, e.g. 0?
>>
>> I couldn't find a way to do this properly in ImageJ...one ugly workaround
>> I
>> came up with is to save the image as text and then simply find & replace
>> all
>> occurences of NaN, but that's not a feasible option for large
>> stacks...there
>> MUST be a better way.
>>
>> Thanks!
>>
>

[BenTupper]

Hi,

On Mar 23, 2011, at 1:03 PM, mjlm wrote:

> Hi there,
>
> Is there a simple way to "reset" all pixels with the value "NaN" to a
> specified numeric value, e.g. 0?
>

A simple way is to use this macro...

newValue = 0.0;
counter = 0;
for (y = 0; y < getHeight(); y++){
        for (x = 0; x < getWidth(); x++){
                p = getPixel(x,y);
                if (isNaN(p)) {
                        setPixel(x, y, newValue);
                        counter++;
                }
        }
}

print("" + counter + " pixels replaced");


Cheers,
Ben

> I couldn't find a way to do this properly in ImageJ...one ugly  
> workaround I
> came up with is to save the image as text and then simply find &  
> replace all
> occurences of NaN, but that's not a feasible option for large  
> stacks...there
> MUST be a better way.
>
> Thanks!
>
> --
> View this message in context: http://imagej.588099.n2.nabble.com/Replace-NaN-in-32-bit-images-with-0-tp6201020p6201020.html
> Sent from the ImageJ mailing list archive at Nabble.com.

[Cammer, Michael]

See http://rsbweb.nih.gov/ij/developer/macro/functions.html#isNaN


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Schmid
Sent: Wednesday, March 23, 2011 1:40 PM
To: [hidden email]
Subject: Re: Replace NaN in 32-bit images with 0

Hi anonymous,

this may look stupid, but it works at least with the NaN created by  
division by zero:
Enter in the Process>Math>Macro
     if (!(v<1) && !(v>0)) v=0;

A NaN value fulfills no inequality; all 'true' numbers are either <1  
or >0 or both.
Of course, a macro function 'isNaN(value)' would be nice to have...

Michael
________________________________________________________________

On 23 Mar 2011, at 18:03, mjlm wrote:

> Hi there,
>
> Is there a simple way to "reset" all pixels with the value "NaN" to a
> specified numeric value, e.g. 0?
>
> I couldn't find a way to do this properly in ImageJ...one ugly  
> workaround I
> came up with is to save the image as text and then simply find &  
> replace all
> occurences of NaN, but that's not a feasible option for large  
> stacks...there
> MUST be a better way.
>
> Thanks!

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[Jeffrey B. Woodward]

The best (most readable) option is to use Double.isNaN(v); however, if
you are looking for a "clever" inequality that is "more correct" and
simpler than the one suggested by Michael Schmid, you can simply test
whether or not v == v...which is only false for NaN. In summary:

Best option:
     if (Double.isNaN(v)) v = 0;

"Clever"/obscure option:
     if (v != v) v = 0;

-Woody


On 3/23/2011 1:40 PM, Michael Schmid wrote:

> Hi anonymous,
>
> this may look stupid, but it works at least with the NaN created by
> division by zero:
> Enter in the Process>Math>Macro
>     if (!(v<1) && !(v>0)) v=0;
>
> A NaN value fulfills no inequality; all 'true' numbers are either <1
> or >0 or both.
> Of course, a macro function 'isNaN(value)' would be nice to have...
>
> Michael
> ________________________________________________________________
>
> On 23 Mar 2011, at 18:03, mjlm wrote:
>
>> Hi there,
>>
>> Is there a simple way to "reset" all pixels with the value "NaN" to a
>> specified numeric value, e.g. 0?
>>
>> I couldn't find a way to do this properly in ImageJ...one ugly
>> workaround I
>> came up with is to save the image as text and then simply find &
>> replace all
>> occurences of NaN, but that's not a feasible option for large
>> stacks...there
>> MUST be a better way.
>>
>> Thanks!

--
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[mjlm]

Cheers to everyone for the quick help!