Posted by
lechristophe on
Jan 29, 2019; 1:27pm
URL: http://imagej.273.s1.nabble.com/reading-roi-files-outside-ImageJ-tp5021725p5021728.html
Dear Kenneth,
The macro below should do what you want - it opens all rois inside a folder
and exports the x,y coordinates as a .csv file (on line per x,y point). I
there is a problem with formatting you can find the macro here also:
http://neurocytolab.org/up/ExportRoi.ijmmacro "ExportROI" {
inputdir = getDirectory("Choose a directory containing .roi files");
filelist = getFileList(inputdir);
for (i = 0; i < filelist.length; i++) {
currfile = filelist[i];
l = lengthOf(currfile);
shortname = substring(currfile, 0, l-4);
ext = substring(currfile, l-4, l);
if (ext == ".roi") {
open(inputdir + currfile);
getSelectionCoordinates(xpoints, ypoints);
string = "";
for (j = 0; j < xpoints.length; j++) {
string = string + "" + xpoints[j] + "," + ypoints[j] + "\n";
}
outname = shortname + ".csv";
File.saveString(string,inputdir + outname);
close();
}
}
}
Christophe
On Mon, 28 Jan 2019 at 23:06, Kenneth Sloan <
[hidden email]> wrote:
> I'm collaborating on a project. My collaborator has created many, many
> .roi files (each one containing a single PolygonRoi).
> I can drag&drop the .roi file on FIJI, and use File->Save As->XY
> Coordinates to get a .txt file that I can read in a non-ImageJ
> Java program.
>
> But, this will be tedious. Is there a simple way to automate this?
>
> a) first choice: is there a description of the .roi file format? Given
> sufficient documentation, I'm comfortable
> writing code to read the .roi file directly
> b) second choid: a SIMPLE macro that will read all of the .roi files in a
> directory and create .txt files containing the XY coordinates.
>
> I'm a skilled Java progammer - but very much a novice at ImageJ macros. I
> expect that my major stumbling block would be
> writing a macro to read in all of the .roi files, one at a time. I think
> I could save to .txt files just fine, once
> I have the .roi file read in. [ I know this is trivial for many of you -
> have pity on me. ]
>
> For scale - I anticipate approximately 60 .roi files. Not out of the
> question to simply do one at a time, by hand - but
> (if it's simple) I'd rather let a macro do the iteration.
>
> --
> Kenneth Sloan
>
[hidden email]
> Vision is the art of seeing what is invisible to others.
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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