doCommand() with user defined functions

Image Analysis
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#1

Hi All,

It seems like doCommand() can only be used on menu functions, but would be helpful to use it to multitask user macros. For example, after completing some conversion on a folder, the macro could go start both the next folder conversions and process converted tiffs in first folder. The computer I am using has 24 cores.

Thanks!
Best,
Ferdinando

1 Like
#2

Hi @Fepu,

you can save whatever macro you want to run in a subfolder of ./Fiji.app/scripts/ and it will appear in the menus (and therefore be callable with doCommand).
For example, if you save your macro at ./Fiji.app/scripts/Plugins/My_Macro.ijm, you can call it with:

doCommand("My Macro");

Hope that helps.

1 Like
#3

Thanks @imagejan it does help. I will need to figure out how to pass variables to the macro though. This is what I’m trying to do:

cohort = getDirectory("Select the cohort folder containing slide folders");
suffix = ".svs";
setBatchMode(true);
run("Bio-Formats Macro Extensions");
slidelist = getFileList(cohort);
Array.sort(slidelist);

// ### FOLDERS ###
// Registered folder under cohort (main folder)
reg = cohort+"Reg"+File.separator;
if (!File.exists(reg)) {
	File.makeDirectory(reg);
}
// output folder under cohort (main folder)
tiff = cohort+"Tiff"+File.separator;
if (!File.exists(tiff)) {
	File.makeDirectory(tiff);	
}

// ### 
// s as in slide
for (s=1; s<slidelist.length+1; s++) {
	filelist = getFileList(cohort+slidelist[s-1]);
	Array.sort(filelist);
	// m as in marker
	for (m=1; m<filelist.length+1; m++) {
		// avoids files in Tiff and Reg folder
		if(endsWith(filelist[m-1], suffix)) {
			// make same name folders under Tiff folder
			if (!File.exists(tiff+slidelist[s-1])) {
				File.makeDirectory(tiff+slidelist[s-1]);	
			}
			if (!File.exists(tiff+slidelist[s-1]+File.separator+filelist[m-1]+".tif")) {
				print("Opening: "+slidelist[s-1]+File.separator+filelist[m-1]);
				Ext.openImagePlus(cohort+slidelist[s-1]+File.separator+filelist[m-1]);
				run("Stack to RGB");
				saveAs("Tiff", tiff+slidelist[s-1]+File.separator+filelist[m-1]+".tif");
				close("*");
			}
		}
	}
	// make same name folders under Reg folder
	if (!File.exists(reg+slidelist[s-1])) {
		File.makeDirectory(reg+slidelist[s-1]);	
	}
	// get reference file name for registration (first Hem?)
	for (m=1; m<filelist.length+1; m++) {
		if (matches(filelist[m-1], "C01R1")) {
			ref = filelist[m-1];
			break;
		}
	}
	// THIS KEEPS POPPING A GUI FOR REF FILE
	run("Register Virtual Stack Slices", "Source directory="+tiff+slidelist[s-1]+" target_dir="+reg+slidelist[s-1]+"  reference_name="+ref+" use_shrinking_constraint=false");
}

I would like to run Register Virtual Stack Slices as a separate thread, to take advantage of the multicore workstation I’m using. I do not know Jython, Java, Matlab, … so any solution involving switching scripting language would have a steep learning curve for me. I still have issues with that command anyway, as you see in the code above (and in this thread)…

Thank you!

Best,
Ferdinando

#4

@imagejan would you mind suggesting how to pass variables to installed macros?

I can call a macro with doCommand("My Macro"); but if I call a var inside the macro it reports undefined variable. Also declaring it as global var does not work. Thank you