Read .rcpnl and output 4 channel tif with subsetting capibility

YC_20180802_C1_Macro-SAVEALLCYCLES02.ijm

// Save color hyperstack into individual tiff(4ch) & Montage with Flat-field
// 20161210 Jerry Lin

myDIR2 = getDirectory("Please enter directory");
myname = getString("Please enter image name","Tonsil1");

cs = getNumber("Enter start cycle:",0);
ce = getNumber("Enter end cycle:",12);


//myDIR2 = myDIR2+"\\";

//mycycle = getString("Please enter the Cycle","4");
//mycycle = "Cycle"+mycycle;

//myDIR = "F:\\"+myname+"\\"+mycycle+"\\";
//myDIR2 = "F:\\"+myname+"\\";

cols= getNumber("Please enter cols:", 32);
rows =  getNumber("Please enter rows:",10);
ch = getNumber("Please enter channels:",4);

startT = getTime;

setBatchMode(true);

for(cyc = cs;cyc<=ce;cyc++){

print("Now processing Cycle "+cyc+"....");

mycycle = "Cycle"+cyc;
myDIR = myDIR2+"\\";

run("Bio-Formats", "open="+myDIR2+mycycle+".rcpnl color_mode=Composite concatenate_series open_all_series view=Hyperstack stack_order=XYCZT");

//rname & making folder

rename(myname);
File.makeDirectory(myDIR);

// Background substraction & splitting channels

// run("Subtract Background...", "rolling=50 sliding disable");
run("Flip Vertically");
name=getTitle;

print ("open file:"+myname+"Cycle"+cyc+" time ="+(getTime-startT)/100);

// Making montage & save image

// run("Make Montage...", "columns="+cols+" rows="+rows+" scale=0.20 increment=1 border=0 font=12");
// rename("Montage-"+myname+"-"+mycycle);
// run("Save", "save="+myDIR2+"Montage-"+myname+"-"+mycycle+".tif");
// close();

//---------------------------------START SAVING TIF FILES-----------------------

selectWindow(myname);
name = getTitle;
n = nSlices;
imagesPerRow = cols*4;

//ch =4;

j=0;
numOfCol = 10;
for (k=0; k<numOfCol; k++) {
	currentRow = k;
	currentRowStartingSlideNum = k*imagesPerRow;
	print("current row = " + k);
	// +40 to move to a more interesting region
	// +4 to generate the even tile
	// +0 to generate the odd tile
	for (i=1+40+0; i<ch*2*numOfCol-1+40+0; i=i+ch*2) {
		selectWindow(name);
		currentSliceNumber = i + currentRowStartingSlideNum;
		setSlice(currentSliceNumber);
		print("current Cycle "+cyc+" slice ="+currentSliceNumber);
		run("Duplicate...", "title="+name+"-"+j);
		outputFName = name+"-"+"row"+IJ.pad(k+1, 3)+"_col"+IJ.pad(j%numOfCol+1, 3)+".tif";
		print(outputFName);
		run("Save", "save=" + myDIR + outputFName);
		selectWindow(outputFName);
		run("Close");
		j++;
	} //end i;
	
} //end k;
close();
print ("Saving image files:"+myname+"Cycle"+cyc+" time ="+(getTime-startT)/1000);
}  //end cyc;

setBatchMode(false);