Zero padding / median filtering - image-processing

Question

I'm trying to implement median filtering using image j .
I am having trouble with the zero padding as it adds extra zeros to the bottom and far left of the picture.
This is what I have done so far, if you guys can help me out:
Dialog.create("9x9 median filtering");
Dialog.addMessage("9x9 median filtering");
Dialog.show();
setBatchMode(true);
median_filter_9();
setBatchMode("exit and display");
// Produce the 9x9 median image
function median_filter_9()
{
width = getWidth();
height= getHeight();
//if you want to apply this median filter to 16bit
depth = bitDepth();
nBin= pow(2, depth);
//nBin hold max gray intensity value
filteHisto = newArray(nBin);
//filteHisto = newArray(255);
fiveBYFive = newArray(81);
//this is what i used for middle position of array to get median
middlePos = round(81/2);
//-3, -3 will get you position 0,0 of a 9x9 matrix if you start in the middle
for(j=-2;j<width-2;j++){
for(i=-2;i<height-2;i++){
z=0;
for(r=0;r<9;r++){
for(c=0;c<9;c++){
//Extend outside image boundaries using zero padding.
//error here: adds extra to bottom and farleft of picture
if(j+r<0||j+r>=width||i+c<0||i+c>=height){
fiveBYFive[z]=0;
z++;
}else{
v = getPixel(j+r,i+c);
fiveBYFive[z]= v;
z++;
}
}
}
//sort the array to find median
Array.sort(fiveBYFive);
median = fiveBYFive[middlePos];
setPixel(j, i, median);
}
updateDisplay();
}
}

Answer 1

One problem you're seeing at the edges of your image is because you are padding your 9x9 window with zeroes ok, but you still take the median value as the middle of the 81 item window.
So, for example, in the first column of the image, you zero-pad at least 36 elements (more at the top and bottom), which means that you only need to find 4 or 5 more zero pixels in the image to make the median element zero.
The easiest fix is to adjust your median element's index (initialised to 81/2 on each iteration) upward according to how many zeroes you added, or just count how many non-zero pixels you used and then find the median mid-way through that range in your sorted array (taking account of sort order).
In this way, you take the median value of the actual pixels you found and ignore the padded zeroes.
Probably, you missed changing your code from the original 5x5 to 9x9, because the start/end indices are in any case wrong and should be
for(j=-4;j<width;j++){
for(i=-4;i<height;i++){
The other possible source of confusion later is with this line, where it looks like you've confused width and height
if(j+r<0||j+r>=width||i+c<0||i+c>=height)
If j is the column index and i is the row index, it should be
if(j+c<0||j+c>=width||i+r<0||i+r>=height)
Although for a square window this doesn't actually make any difference in practice.