Re: ImageJ Command Line Run Arguements

Posted by ctr26 on Oct 21, 2015; 6:48pm
URL: http://imagej.273.s1.nabble.com/ImageJ-Command-Line-Run-Arguements-tp5014676p5014707.html

I solved it for myself.

**************** Macro code ****************
cmd = getArgument();
string = split(cmd, ",");
print(cmd);
order =  string[0];
channels = parseInt(string[1]);
slices =  parseInt(string[2]);
frames =  parseInt(string[3]);
dir = getDirectory("image")
file = getInfo("image.filename")
print("Creating hyper Stack");
print(dir+file)
run("Stack to Hyperstack...", "order=&order channels=&channels slices=&slices frames=&frames display=Color");
print("Saving");
saveAs("Tiff", dir + file);
print("Fin");
*********************************************

Which takes a single string argurment delimited by commas.


*****************Batch file*********************
setlocal
cd /d %~dp0
java -jar ij.jar -open test.tif -batch hyper.ijm "xyczt(default),0001,0005,0002"
*********************************************

This is the batch that converts tif stacks to hyperstacks.