I've been playing with your macro and it looks like an ImageJ bug. For some
You might want to use a script instead. It's a bit of more work but you'll
> Hi
> I had successfully been using a image analyzeskeleton plugin to
> skeletonize and then produce two output files, results and branch
> information. When I run the following code from inside the macro editor, I
> get two files saved, BranchInformation_1.txt and resultstable_2, and they
> are different. i.e. BranchInfo contains headings (skeleton, branch length,
> vx,vy etc) and resultstable_2 has (#branches, #junctions, #endpoint etc).
>
> I call the macro from a windows cmd prompt with
>
> java -jar C:\Users\Russell\Downloads\fiji-win32\Fiji.app\jars\ij-1.49m.jar
> -batch Macro1
>
> When running it as part of a batch file, it saves the two output files,
> but they have identical content, that is both file are equal to
> BranchInformation_1.txt.
> I can go back and forwards confirming that the content changes with
> whether it is called from a cmd prompt or not.
>
> So, my questions is whether there is a way to reliably save the two files
> that are created by plugin analyse skeleton? Or am I missing something?
>
> Thanks in advance.
>
> Russell
>
> arg_array = newArray(3) // I am planning to pass some arguments in the
> future
> arg_array[0] = 1;
> arg_array[1] = 2;
>
> name1 = "BranchInformation_" + arg_array[0] +".txt";
> name2 = "ResultsTable_" + arg_array[1] +".txt";
>
> open("C:\\c6work \\Test.jpeg"); // this is the image I want to analyse
> run("8-bit");
> run("Auto Threshold", "method=Huang ignore_black ignore_white white");
> run("Auto Threshold", "method=Default");
> run("Skeletonize (2D/3D)");
>
> wait(2000); // added because I thought a delay might help
>
> run("Analyze Skeleton (2D/3D)","prune=none show");
>
> saveAs("results",
> "C:\\Users\\Russell\\Downloads\\fiji-win32\\Fiji.app\\output\\macros\\" +
> name2);
> saveAs("measurements",
> "C:\\Users\\Russell\\Downloads\\fiji-win32\\Fiji.app\\output\\macros\\" +
> name1);
> //end of macro
>
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