On Oct 31, 2011, at 10:48 AM, Christophe Leterrier wrote:
> Hi,
>
> I'm writing a script that does the following : I have a smoothened lined
> obtained with the "Fit Spline" command on a line selection.
> I get the intensity profile along this line, and based on that profile the
> script detects a part of the ROI as the object of interest. Let's say that
> on the profile view, the ROI is 500 pixels long (p=0 to p=500) and that the
> detected object is 200 pixels long (from p=100 to p=300).
>
> Now I would like to trace this detected object on the original image. But i
> need to get the coordinates of the detected object as XY image coordinates
> from its coordinates along the profile. How could I do that ?
>
> - First, I'm sure this has been discussed before, but I can't find the
> method that gives all XY coordinates of a line ROI as two X,Y arrays, 1
> pixel appart (in my exemple it should give me two arrays whose length is
> 500, one containing the X coordinates and the other one the Y coordinates).
> - Once I get that, It will be easy to use the profile coordinate as an
> index to find the corresponding X,Y coordinates.
Use the "straighten" option of "Fit Spline" to get one pixel spacing and the getSelectionCoordinates() macro function or getFloatPolygon() method to get the coordinates as two arrays. Here is a macro example:
run("Fit Spline", "straighten");
getSelectionCoordinates(x, y);
x2=0; y2=0; distance=0;
for (i=0; i<x.length; i++) {
if (i>0) {
dx = x[i] - x[i-1];
dy = y[i] - y[i-1];
distance = sqrt(dx*dx+dy*dy);
}
print(i, x[i], y[i], distance);
}
And here is a JavaScript version:
imp = IJ.getImage();
IJ.run("Fit Spline", "straighten");
roi = imp.getRoi();
p = roi.getFloatPolygon();
x2=0; y2=0; distance=0;
for (i=0; i<p.npoints; i++) {
if (i>0) {
dx = p.xpoints[i] - p.xpoints[i-1];
dy = p.ypoints[i] - p.ypoints[i-1];
distance = Math.sqrt(dx*dx+dy*dy);
}
x = IJ.d2s(p.xpoints[i],2);
y = IJ.d2s(p.ypoints[i],2);
d = IJ.d2s(distance,2);
print(i+" "+x+" "+y+" "+d);
}
-wayne
Locked
