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_DKR_Scale&RGB_Batch.ijm
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_DKR_Scale&RGB_Batch.ijm
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// created by Dan Rozelle 20110324
//used to create a similarly scaled montage for each image in a file
//this will only work with flat composite images (multi channel, single slice)
macro "go [q]"{
setBatchMode(false);
if(nImages>0) exit ("close all images before proceeding");
if(isOpen("Results")){
selectWindow("Results");
run("Close");
}
if(isOpen("Log")){
selectWindow("Log");
run("Close");
}
//list auto functions here, adjust mode as necessary
function batchfunction();
/**********************************************************/
Dialog.create("Select Options");
Dialog.addString("Filter","tif");
Dialog.addString("Channel 1", "Blue");
Dialog.addNumber("Min", 456);
Dialog.addNumber("Max", 1150);
Dialog.addString("Channel 2", "Red");
Dialog.addNumber("Min", 396);
Dialog.addNumber("Max", 1036);
Dialog.addString("Channel 3", "Green");
Dialog.addNumber("Min", 412);
Dialog.addNumber("Max", 706);
Dialog.addString("Channel 4", "empty");
Dialog.addNumber("Min", 853);
Dialog.addNumber("Max", 1308);
Dialog.addMessage("specify Channel= 'empty' for fewer channels, use \"-1\" to turn that channel off. Use Min/Max = -1 to autoscale that channel ");
Dialog.show();
filter=Dialog.getString();
//make 3 arrays for the color and settings of each channel
color = newArray("empty","empty","empty","empty");
min = Array.copy(color);
max = Array.copy(color);
//loop through the input dialog and capture their values
for(i=0;i<4;i++){
color[i]=Dialog.getString();
min[i] = Dialog.getNumber();
max[i] = Dialog.getNumber();
}
/**********************************************************/
//find the source images
dir1 = getDirectory("Choose source directory");
if (dir1=="")
exit("No directory available");
parent = File.getParent(dir1);
// Create an output directory within dir1
dir2 = parent+File.separator+"RGB"+File.separator;
File.makeDirectory(dir2);
if (!File.exists(dir2))
exit("Unable to create directory");
// print("dir1 = "+dir1);
// print("parent = "+parent);
// print("dir2 = "+dir2);
//filter files necessary
if(filter == ""){
list = getFileList(dir1);
}
else{
//get a list of all the files in this folder
preList = getFileList(dir1);
size=0;
//count each '*filter*' files
for(place=0;place<preList.length;place++){
if(endsWith(preList[place],filter)){
size++;
}
}
//create a new array and populate with filtered images
list=newArray(size);
position=0;
for(place=0;place<preList.length;place++){
if(endsWith(preList[place],filter)){
list[position]=preList[place];
position++;
}
}
}
//starting with the first image, we increment through each image, performing the batch function
for(i=0; i<list.length; i++){
showProgress(i+1/list.length);
//this will not work if this is still a stack, however a single plane SNAP will work fine
if(filter != 'tif'){
run("Bio-Formats Importer", "open="+dir1+list[i]+" view=Hyperstack stack_order=XYCZT");
}
else{
open(dir1+list[i]);
}
selectWindow(list[i]);
//perform the batch function
batchfunction(list[i]);
//close the window after returning from function
selectWindow(list[i]);
close();
}
}
function batchfunction(name){
selectWindow(name);
//repeat loop for each channel j
getDimensions(width, height, channels, slices, frames);
stop = channels;
for(j=0;j<stop;j++){
setSlice(j+1);
if(color[j] != "empty" && color[j] != -1){
run(color[j]);
//print(j+" = "+color[j]+",min="+min[j]+", max="+max[j]);
if(min[j] != -1){
setMinAndMax(min[j], max[j]);
call("ij.ImagePlus.setDefault16bitRange", 16);
}
else{
run("Enhance Contrast", "saturated=0.35");
}
}
}
selections = "";
for(j=0;j<stop;j++){
if(color[j] == -1){selections += 0;}
else {selections += 1;}
}
run("RGB Color");
selectWindow(name+" (RGB)");
saveAs("Tiff", dir2+"RGB_"+name);
close();
}