Re: Threshold as a percentage of image histogram?

Posted by Ben Tupper on Jul 03, 2008; 11:54am
URL: http://imagej.273.s1.nabble.com/Threshold-as-a-percentage-of-image-histogram-tp3695671p3695673.html

On Jul 3, 2008, at 3:03 AM, Roger Chang wrote:

> Ben,
> Thanks for your suggestion and corresponding code. I did not  
> realize that
> there was the macro function getHistogram(counts, values,  
> nBins, ...). I
> adopted your macro to instead calculate a threshold as a function of a
> percentage of the total area under an image histogram. It  
> calculates the
> total number of pixel values in the image histogram. Then it makes  
> a new
> cumulative array of the count array, such that the tissueValue  
> (equals total
> number of pixel values * the tissueThreshPercentage) can be found  
> within the
> cumulative array and a threshold can be outputted:
>
> // Input a tissue threshold percentae 0-100
> tissueThreshPrec = 80;
> nBins = 256;
> getHistogram(values, count, nBins);
> size = count.length;
> // find culmulative sum
> cumSum = 0;
> for (i = 0; i<count.length; i++)
> {
> cumSum += count[i];
> }

Hi Roger,

The only suggestion I have for you is to consider that for 8-bit and  
RGB images the total "area" under the histogram is the number of  
pixels in the image.  This is a design implementation specific to  
ImageJ.  Thus you can skip the "cumSum" loop above to calculate the  
total number of pixels and go directly to ....

totalNumberOfPixels = getWidth() * getHeight();


Cheers,
Ben

> tissueValue = cumSum * tissueThreshPerc / 100;
> print(tissueValue);
> // cumulative sum of before
> cumSumValues = count;
> for (i = 1; i<count.length; i++)
> {
> cumSumValues[i] += cumSumValues[i-1];
> }
>
> // find tissueValue
> for (i = 1; i<cumSumValues.length; i++)
> {
> if (cumSumValues[i-1] <= tissueValue && tissueValue <= cumSumValues
> [i])
> // output tissue threshold:
> print(i);
> }
>
> Hopefully my macro makes sense.
> -Roger C.

Ben Tupper
[hidden email]

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