Posted by
Christopher Coulon-2 on
Jul 15, 2008; 2:27am
URL: http://imagej.273.s1.nabble.com/Get-continuous-pixel-coordinates-from-a-line-ROI-tp3688036p3688047.html
Here¹s a macro and plugin that give the complete coordinates of a polygon
selection (closed or line).
Chris Coulon
The GAIA Group
Global Automated Image Analysis
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Christopher Coulon, Ph.D., Founder
http://gaiag.net[hidden email]
macro "Get all line coordinates [f1]" {
sum = 0;
count = 0;
getSelectionCoordinates(x, y);
len = x.length;
x1 = newArray(len);
y1 = newArray(len);
hypot = newArray(len);
//print("\n**********\ni x[i] y[i] x1[i] y1[i] hypot");
for (i = 1; i < len; i++) {
x1[i] = x[i-1] - x[i];
y1[i] = y[i-1] - y[i];
hypot[i] = sqrt(x1[i] * x1[i] + y1[i] * y1[i]);
sum += hypot[i];
//print(i + " " + x[i] + " " + y[i] + " " + x1[i] + " " + y1[i] +
" " + hypot[i]);
}
fullPerimX = newArray(sum);
fullPerimY = newArray(sum);
for (i = 0; i < len; i++) {
if(x1[i] != 0) {
n = x1[i];
if(n < 0) {
for(j = n; j < 0; j++) {
fullPerimX[count] = x[i] + j;
fullPerimY[count] = y[i];
count++;
}
}
else {
for(j = n; j > 0; j--) {
fullPerimX[count] = x[i] + j;
fullPerimY[count] = y[i];
count++;
}
}
}
else {
if(y1[i] != 0) {
n = y1[i];
if(n < 0) {
for(j = n; j < 0; j++) {
fullPerimY[count] = y[i] + j;
fullPerimX[count] = x[i];
count++;
}
}
else {
for(j = n; j > 0; j--) {
fullPerimY[count] = y[i] + j;
fullPerimX[count] = x[i];
count++;
}
}
}
}
}
print("\ncount = " + count + "\n***** Full Line Coordinates *****\n");
print("Position X Y");
for (i = 0; i < count; i++) {
if(i < 10)
print(" " + i + " " + fullPerimX[i] + " " +
fullPerimY[i]);
else
if(i < 100)
print(" " + i + " " + fullPerimX[i] + " " +
fullPerimY[i]);
else
print(" " + i + " " + fullPerimX[i] + " " +
fullPerimY[i]);
}
}
import ij.IJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.gui.PolygonRoi;
import ij.gui.Roi;
import ij.measure.Calibration;
import ij.plugin.PlugIn;
import java.awt.Rectangle;
/**
* © 2008 The GAIA Group
* Christopher Coulon, PhD
*
http://gaiag.net */
public class A_Line_Roi implements PlugIn
{
public void run(String arg0)
{
if(WindowManager.getImageCount() < 1)
{
IJ.error("No Images Open!");
return;
} // if count < 1
ImagePlus imp = WindowManager.getCurrentImage();
Calibration cal = imp.getCalibration();
double pixW = cal.pixelWidth;
double pixH = cal.pixelHeight;
int len = 0;
int sum = 0;
int counter = 0;
int n = 1;
Roi line = imp.getRoi();
if(line == null)
{
IJ.error("No Polygon Selection!");
return;
} // if line
Rectangle bounds = line.getBounds();
int xBound = bounds.x;
int yBound = bounds.y;
if(line instanceof PolygonRoi)
{
PolygonRoi proi = (PolygonRoi)line;
len = proi.getNCoordinates();
int[] hypot = new int[len];
int[] x1 = new int[len];
int[] y1 = new int[len];
int[] xCoords = proi.getXCoordinates();
double[] xProi = new double[len];
int[] yCoords = proi.getYCoordinates();
double[] yProi = new double[len];
for (int i = 0; i < len; i++) {
xProi[i] = pixW*xCoords[i] + xBound;
yProi[i] = pixH*yCoords[i] + yBound;
if(i > 0)
{
x1[i] = (int) (xProi[i - 1] - xProi[i]);
y1[i] = (int) (yProi[i - 1] - yProi[i]);
hypot[i] = (int) Math.sqrt(x1[i] * x1[i] + y1[i] *
y1[i]);
sum += hypot[i];
} // if i
} // for i
int[] fullPerimX = new int[sum];
int[] fullPerimY = new int[sum];
for (int i = 0; i < len; i++)
{
if(x1[i] != 0)
{
n = x1[i];
if(n < 0)
{
for(int j = n; j < 0; j++)
{
fullPerimX[counter] = xCoords[i] + j + xBound;
fullPerimY[counter] = yCoords[i] + yBound;
counter++;
} // for j
} // if n
else
{
for(int j = n; j > 0; j--)
{
fullPerimX[counter] = xCoords[i] + j + xBound;
fullPerimY[counter] = yCoords[i] + yBound;
counter++;
} // for j
} // else
} // if x1
else
{
if(y1[i] != 0)
{
n = y1[i];
if(n < 0)
{
for(int j = n; j < 0; j++)
{
fullPerimY[counter] = yCoords[i] + j +
yBound;
fullPerimX[counter] = xCoords[i] + xBound;
counter++;
} // for j
} // if n
else
{
for(int j = n; j > 0; j--)
{
fullPerimY[counter] = yCoords[i] + j +
yBound;
fullPerimX[counter] = xCoords[i] + xBound;
counter++;
} // for j
} // else
} // if y1
} // else
} // for i
IJ.log("**** Full Line Coordinates ****\n" +
"\nPosition X Y\n");
for (int i = 0; i < sum; i++)
{
if(i < 10)
IJ.log(" " + i + " " +
fullPerimX[i] +
" " + fullPerimY[i]);
else
if(i < 100)
IJ.log(" " + i + " " +
fullPerimX[i] +
" " + fullPerimY[i]);
else
IJ.log(" " + i + " " +
fullPerimX[i] +
" " + fullPerimY[i]);
} // for i
} // if roi
else
{
IJ.showMessage("Only Polygon ROIs are processed");
return;
} // else
} // run method
} // A_Line_Roi class
>
> Damn, you're right !
> For the shrinking line, the problem was that the macro doesn't handle
> the last point (corrected).
> For the duplicate points, I had to revert to Michael strategy
> (although I'll also try just to add a test for creation of the same
> point for Chris strategy). The new version is here :
>
>
https://www.bio.espci.fr/upload/files/All_Coordinates2.txt>
>
>
> Christophe
>
>
> On Sun, Jul 13, 2008 at 11:40, Gabriel Landini <
[hidden email]> wrote:
>> > On Saturday 12 July 2008, Christophe Leterrier wrote:
>>> >> I modified a macro proposed by Michael Cammer that was quite
>>> >> complicated
>>> >>
>>> (
http://www.nabble.com/Re%3A-List-all-pixel-coordinates-in-ROI-p529148.html>>> >>). Thanks to Chris Coulon who proposed a slightly different strategy, that
>>> >> is just get the distance between each vertices and increment with
>>> subpixel
>>> >> distance between these two points, I managed to get a simpler second
>>> >> version wich I append here :
>>> >>
>>> >>
https://www.bio.espci.fr/upload/files/All_Coordinates.txt>>> >>
>>> >> Hope it will be usefull for others,
>> >
>> > I am not sure the reason, but I think this may not be working as intended:
>> > 1. the line it gets shorter by 1 each time the macro runs,
>> > 2. for diagonal lines, some points are repeated (usually the 2nd point from
>> > the start is 2 points overlapping rather than 1).
>> >
>> > Can anybody confirm this? It is easier to try this with short lines and the
>> > image zoomed in).
>> > Cheers
>> >
>> > Gabriel
>> >