Your problem is in getPixel which does not yield a color written in hex.
I present to you your best friend on ImageJ : the built-in macro functions code
https://imagej.nih.gov/ij/developer/macro/functions.html
which documents built-in pixel functions such as getPixel().
For getPixel(), it is stated "Note that pixels in RGB images contain red, green and blue components that need to be extracted using shifting and masking. See the Color Picker Tool macro for an example that shows how to do this. ", and the Color Picker Tool macro tells us how to go from color "bits" to RGB.
So if you wish to compare colors, you do :
basecolor=newArray(0,0,0);
rightpixel = getPixel(x,y);
//from the Color Picker Tool macro
//converts what getPixel returns into RGB (values red, green and blue)
if (bitDepth==24) {
red = (v>>16)&0xff; // extract red byte (bits 23-17)
green = (v>>8)&0xff; // extract green byte (bits 15-8)
blue = v&0xff; // extract blue byte (bits 7-0)
}
//compare the color with your color
if(red==basecolor[0] && green==basecolor[1] && blue==basecolor[2]){
print("Same Color");
count++;
}
//you can also work with hex by converting the rgb to hex and then
//comparing the strings like you did