x y coords of anchor points on segmented line

[Tobias Baskin]

Hi,
    Is there a way to recover the x-y coordinates of JUST the anchor points on a segmented line? When I do "save as ... xy" I get tons of xy data. But I need only the anchor points (sorry if that is the wrong word - I mean the places where I clicked to define the segments). I tried to search for this but "segmentation" dominates the results. Hoping somone can point me to a useful plugin/macro for this.
Thanks,
          Tobias

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[Volker Baecker]

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Hi Tobias,
in a macro you can do it with:

Roi.getSplineAnchors(xx, yy);
Array.print(xx);
Array.print(yy);

Volker

Tobias Baskin:

> Hi, Is there a way to recover the x-y coordinates of JUST the
> anchor points on a segmented line? When I do "save as ... xy" I get
> tons of xy data. But I need only the anchor points (sorry if that
> is the wrong word - I mean the places where I clicked to define
> the segments). I tried to search for this but "segmentation"
> dominates the results. Hoping somone can point me to a useful
> plugin/macro for this. Thanks, Tobias
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Tobias Baskin]

Volker,
        Thank you. I just tried it and got an error: unrecognized roi function. I simply cut and pasted what you wrote into a new macro and installed it (I didn't 'compile it). I am running version 1. 49m. Sorry I am quite an ImageJ novice, maybe there is something obvious to make the macro you wrote work? Thanks again! Tobias

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[Volker Baecker]

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Hello Tobias,
yes you are right, you need at least version 1.49p.
It is macro code, not a plugin so there is nothing to compile.
You can just copy the code and paste it into ImageJ. It should be
opened in a macro editor where you can run it from the menu Macros>Run
Macro.
Volker

Tobias Baskin:
> Volker, Thank you. I just tried it and got an error: unrecognized
> roi function. I simply cut and pasted what you wrote into a new
> macro and installed it (I didn't 'compile it). I am running version
> 1. 49m. Sorry I am quite an ImageJ novice, maybe there is something
> obvious to make the macro you wrote work? Thanks again! Tobias
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Volker Baecker]

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In fact, I made it to complicated.

Roi.getCoordinates(xx, yy);
Array.print(xx);
Array.print(yy);

should work as well even with older versions of ImageJ.

Volker

Volker Baecker:

> Hello Tobias, yes you are right, you need at least version 1.49p.
> It is macro code, not a plugin so there is nothing to compile. You
> can just copy the code and paste it into ImageJ. It should be
> opened in a macro editor where you can run it from the menu
> Macros>Run Macro. Volker
>
> Tobias Baskin:
>> Volker, Thank you. I just tried it and got an error:
>> unrecognized roi function. I simply cut and pasted what you wrote
>> into a new macro and installed it (I didn't 'compile it). I am
>> running version 1. 49m. Sorry I am quite an ImageJ novice, maybe
>> there is something obvious to make the macro you wrote work?
>> Thanks again! Tobias
>
>> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Tobias Baskin]

Volker,
        Thank you again. I downloaded the latest version and now the ROI.getSplineAnchors runs. Yay! (in the latest version, the ROI.getCoordinates returns points every pixel, not just the anchors). But it happens that the software that I feed the coordinates into needs the y-axis coordinate inverted, and the returned y-values are not inverted. I have the 'invert Y coordinate' checked in the set measurements options but I suppose that the ROI command is not a measure command and hence oblivious to that. Is there a command to add to the macro that will invert the y values? Also, is there syntax to have the data come out as x y, x y, x y, rather than x x x, y y y? That would be quite helpful. I totally appreciate your time here! Many thanks, Tobias

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[Volker Baecker]

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Tobias
does the macro below do what you want?

Roi.getSplineAnchors(xx, yy);
height = getHeight();
print("\\Clear");
result = "";
for(i=0; i<xx.length; i++) {
        result += "" + xx[i] + " " + (height - yy[i]);
        if (i<xx.length - 1) result += ", ";
}
print(result);

Volker

Tobias Baskin:

> Volker, Thank you again. I downloaded the latest version and now
> the ROI.getSplineAnchors runs. Yay! (in the latest version, the
> ROI.getCoordinates returns points every pixel, not just the
> anchors). But it happens that the software that I feed the
> coordinates into needs the y-axis coordinate inverted, and the
> returned y-values are not inverted. I have the 'invert Y
> coordinate' checked in the set measurements options but I suppose
> that the ROI command is not a measure command and hence oblivious
> to that. Is there a command to add to the macro that will invert
> the y values? Also, is there syntax to have the data come out as x
> y, x y, x y, rather than x x x, y y y? That would be quite helpful.
> I totally appreciate your time here! Many thanks, Tobias
>
>

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[Tobias Baskin]

Volker,
         Perfect! Wow! I cannot even pretend to understand the syntax of that do loop. But it certainly works. This will save me a bunch of time (I have been writing down those points by hand!). I am tremendously grateful.

As ever,
         Tobias

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[Volker Baecker]

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It's really not as complicated as it looks.

for(i=0; i<xx.length; i++) {
        result += "" + xx[i] + " " + (height - yy[i]);
        if (i<xx.length - 1) result += ", ";
}

In the for-loop the index i will run from 0 to length of the array xx
minus one. In each iteration the two coordinate values x and y are
added to the result string. The value of y is inverted by subtracting
it from the height of the image.
In each iteration except the last a comma is added to the result string.

Note that "result +="  is short for "result = result  + "

<shameless self-advertisement>

If you want to know more about ImageJ macro programming you can have a
look at my workshop at:

http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/ImageJ_Macro_Programming_for_Biological_Image_Analysis

</shameless self-advertisement>

Volker
Tobias Baskin:
> Volker, Perfect! Wow! I cannot even pretend to understand the
> syntax of that do loop. But it certainly works. This will save me a
> bunch of time (I have been writing down those points by hand!). I
> am tremendously grateful.
>
> As ever, Tobias
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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