Changing pixel values in a stack

[Behdad Pouran]

Dear all,

I'm using FIJI and would like to convert the pixel values between 0 and 25
to 30. I have created the following code but when the stack contains more
than a certain number of slices it fails to cover the whole pixels. Could
you please assist me with this problem? Is there a faster way available?

This is the code:

v1=0;

v2=25;

v3=30;

O=getWidth();

Y=getWidth();

Z=getSliceNumber();

for (k = 1; k <= Z; k++){

for (i = 0; i <= O; i++){

for (j = 0; j <= Y; j++){

changeValues(v1, v2, v3);

}

}

}

Thank you very much in advance.

[michae...@gmail.com]

Hi Behdad,

You should use nSlices() to set your Z variable and also you have to tell your loop which pixel you are changing. At the moment you call changeValues() but with no reference to a location. Look at setPixel() and setSlice() methods.

Michael

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[Richard Domander]

Hi Behdad,

I believe that the loop termination conditions for i and j  should be i < O and j < Y.

In addition the initialization of O should be O = getHeight();

Best Regards,

Richard Domander

[Michael Doube]

Additionally, Z should be initialised to:

Z = nSlices();

getSliceNumber() returns the index of the current slice, not the number of slices in the stack.

See http://rsbweb.nih.gov/ij/developer/macro/functions.html for documentation on macro functions.

For historical reasons, slice numbers start at 1 so you are correct to iterate from 1 to Z inclusive (i.e. with a <=) . But, (x,y) coordinates start at 0 so you must end your row and column loops with < and not <= else you will go beyond the end of the pixel array.

Michael

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