// Created by Ayal Lavi 6/3/2020 ayallavi@g.ucla.edu
setBatchMode(true);
result_header_txt = " - 32-Bit - rescaled (xy) - normalized - score (detections)"
dir = getDirectory("Choose model output folder")
fn_modeldef = File.openDialog("select modeldef file");
print("modeldef filename: " + fn_modeldef);
 imgArray = newArray(nImages);
 fn_weight = "";
 tileX = 200;
 tileY = 200;
 tileZ = 100;
 hostname = "192.168.1.1";
 username = "user";
 
 Dialog.create("UNet Weight file");
 Dialog.addString("UNet weight filename", fn_weight);
 Dialog.addNumber("Tile X", tileX);
 Dialog.addNumber("Tile Y", tileY);
 Dialog.addNumber("Tile Z", tileZ);
 Dialog.addString("hostname", hostname);
 Dialog.addString("username", username);
 Dialog.show();
 fn_weight = Dialog.getString();
 tileX = Dialog.getNumber();
 tileY = Dialog.getNumber();
 tileZ = Dialog.getNumber();
 hostname = Dialog.getString();
 username = Dialog.getString();
 
 print("Weight filename: " + fn_weight);
 print("Tile shape (px)= " + tileX + "x" + tileY + "x" + tileZ);
 print("hostname= " + hostname);
 print("username= " + username);

fn_rsa = File.openDialog("select RSA key file <path_to_RSA_file/id_rsa>");
 print("RSA Key File= " + fn_rsa);
 
 for (i=0; i<nImages; i++) {
 selectImage(i+1);
 imgArray[i] = getImageID(); }
 //now we have a list of all open images, we can work on it:
 for (i=0; i< imgArray.length; i++) {
 selectImage(imgArray[i]);
 img_name = getInfo("image.filename");
 print(img_name);
 // INSERT MACRO HERE
call('de.unifreiburg.unet.DetectionJob.processHyperStack', 'modelFilename=' + fn_modeldef + ',Tile shape (px):='+tileX+'x'+tileY+'x'+tileZ+',weightsFilename='+ fn_weight + ',gpuId=GPU 0,useRemoteHost=true,hostname='+hostname+',port=22,username='+username+',,RSAKeyfile='+fn_rsa+',processFolder=,average=none,keepOriginal=true,outputScores=true,outputSoftmaxScores=false');
 selectWindow(img_name+result_header_txt);
 saveAs("Measurements", dir+img_name+"_out.csv");
 }
 // Created by Ayal Lavi 6/3/2020 ayallavi@g.ucla.edu