Re: Percentile value

Posted by Wayne Rasband on Jun 11, 2009; 8:33pm
URL: http://imagej.273.s1.nabble.com/Percentile-value-tp3690983p3690987.html

> Hi all,
>
> To get the percentile value, I think that I could get all the pixel
> value by using getpixel (I,j) and make an array.
> Then I need to sort the array. How do I sort the array using ImageJ
> macro language? Do you have to make a function?

Use the Array.sort() macro function to sort an array. Here is an
example macro that creates an array from all pixels in an image then
sorts the array:

    requires ("1.42j");
    w = getWidth;
    h = getHeight;
    a = newArray(w*h);
    i = 0;
    for (y=0; y<h; y++)
       for (x=0; x<w; x++)
           a[i++] = getPixel(x,y);
    Array.sort(a);

-wayne

> Thanks!
>
> Zhengyu
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Pang, Zhengyu (GE, Research)
> Sent: Thursday, June 11, 2009 10:15 AM
> To: [hidden email]
> Subject: Re: Percentile value
>
> Ben,
>
> Thanks for your help. I tested your macro and it worked. As you said,
> this is only an approximation.
>
> I am wondering if ImageJ could read an image and then convert image to
> a
> matrix like what Matlab can do. Could you then sort the matrix and
> found
> 5% percentile?
>
> Best Regards,
>
> Zhengyu
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Ben Tupper
> Sent: Wednesday, June 10, 2009 8:34 PM
> To: [hidden email]
> Subject: Re: Percentile value
>
> Hi,
>
> On Jun 9, 2009, at 11:19 AM, Pang, Zhengyu (GE, Research) wrote:
>
>> Dear all,
>>
>> ImageJ could provide you with Mean, median, min and max. How do I get
>> 1 percentile, or 5 percentile values? And how do I get the average for
>
>> first percentile.?
>>
>
> I Wonder if the cumulative histogram (normalized) could work for you.
> The following converts the histogram to a cumulative histogram, then
> normalizes it to the number of pixels in the image.   I'm no stats
> guy, so this might be considered an approximation by purists.
>
> Cheers,
> Ben
>
> //START MACRO
> //run("Blobs (25K)");
> nBins = 256;
> getHistogram(values, counts, 256);
>
> //create a cumulative histogram
> cumHist = newArray(nBins);
> cumHist[0] = values[counts[0]];
> for (i = 1; i < nBins; i++){ cumHist[i] = counts[i] + cumHist[i-1]; }
>
> //normalize the cumulative histogram
> normCumHist = newArray(nBins);
> for (i = 0; i < nBins; i++){  normCumHist[i] = cumHist[i]/
> cumHist[nBins-1]; }
>
>
> // find the 5th percentile (= 0.05)
> target = 0.05;
> i = 0;
> do {
> i = i + 1;
> print("i=" + i + "  value=" + values[i] +  "  count=" +
> counts[i] + "
> cumHist= " + cumHist[i] + "  normCumHist= " + normCumHist[i] ); } while
> (normCumHist[i] < target)
>
> print("5th percentile located at either " + (i-1) + "th or " + (i) +
> "th
> bin");
> print("    which has a location of " + values[i-1] +" or " +
> values[i]);
>
> //END MACRO
>
>
>
> Ben Tupper
>