// this file show section ocdes with general purpose
// all codes are under my personal preference, please read carefully and adopt for your use.
// A. Initialize ImageJ
// B. Bacth process setup
// C. parameter input
// D. simple print summary


// --------- A. Initialize ImageJ ----------------
// this code section sets image foreground as white, and background for black. 
// it is mostly for fluorescence images. Users should use their preference to set it up.
// this is normally at the begining of the code.

run("Colors...", "foreground=white background=black selection=yellow");
run("Options...", "iterations=1 count=1 black");
run("Set Measurements...", "area mean standard modal min centroid center perimeter bounding fit shape feret's integrated median skewness kurtosis area_fraction stack redirect=None decimal=5");

// ------------ end A Initialize ImageJ ------------

// ----------- B. Bacth process setup  ----------------
// this code provide general set up for bacth process on a signle folder

rawdir=getDirectory("User Choose Raw Data Folder");
resultdir=getDirectory("User Choose Result Data Folder");
list=getFileList(rawdir);
for(f=0;f<list.length;f++)
 {
  // process for each image in the rawdir
 }

// --------- end B. Bacth process setup  ----------------

// --------- C. Parameter input -----------------
// this code shows the function of user input analysis parameters
// check "Dialog" function in ImageJ "built-in" function website for more information
//https://imagej.nih.gov/ij/developer/macro/functions.html#D

function parameter_input()
 {
  Dialog.create("Parameter_input");
  Dialog.addNumber("Number of Channels:", 2);
  Dialog.addNumber("Nuclei MinSize (um^2):", 40);
  Dialog.addNumber("Nuclei MaxSize (um^2):", 700);
  Dialog.addNumber("Object_A MinSize (um^2):", 0.25);
  Dialog.addNumber("Object_A MaxSize (um^2):", 8);
  Dialog.addChoice("Nuclei Threshold Type:", newArray("Otsu dark", "Huang dark", "Default dark", "Triangle dark", "Yen dark", "Sahnbhag dark"));
  Dialog.addChoice("Object_A Threshold Type:", newArray("Triangle dark", "Default dark", "Otsu dark", "Huang dark", "Yen dark", "Sahnbhag dark"));
  
  Dialog.show();

  channels = Dialog.getNumber();
  nuclei_min = Dialog.getNumber();
  nuclei_max= Dialog.getNumber();
  objecta_min = Dialog.getNumber();
  objecta_max = Dialog.getNumber();
  nuclei_method = Dialog.getChoice();
  objecta_method = Dialog.getChoice();
 }

// ----------- end C. Parameter input -----------------


//  ---------- D. simple print summary  ---------------
// base on section C, user should print a summary table to record all the analysis parameters input for certain results

// erase Log window, start new print
print("\\Clear");
print("RawDataFolder:	"+rawdir);
print("Nuclei_Min_Size(um^2)	Nuclei_Max_Size(um^2)	ObjectA_Min_Size(um^2)	ObjectA_Max_Size(um^2)");
print(nuclei_min+"	"+nuclei_max+"	"+objecta_min+"	"+objecta_max);
print("Nuclei_Threshold_Method	ObjectA_Threshold_Method");
print(nuclei_method+"	"+objecta_method);

// save and close Log window
selectWindow("Log"); saveAs("Text", resultdir+"Summary.xls");
selectWindow("Log"); run("Close");

// --------- end  D. simple print summary  ---------------