//SAMA
version=0.99;
//Copyright (C) 2015 Maël Montévil and Tessie Paulose 

//    This program is free software: you can redistribute it and/or modify
//    it under the terms of the GNU General Public License as published by
//    the Free Software Foundation, either version 3 of the License, or
//    (at your option) any later version.

//    This program is distributed in the hope that it will be useful,
//    but WITHOUT ANY WARRANTY; without even the implied warranty of
//    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//    GNU General Public License for more details.

//    You should have received a copy of the GNU General Public License
//    along with this program.  If not, see <http://www.gnu.org/licenses/>.


print("***************************");
print("Sarting R Sama  version "+version);

//function to create a directory if it does not exist
function createdir(dir, suffix) {
  dirres=dir+suffix+"/";
  if(!File.isDirectory(dirres)){
    File.makeDirectory(dirres);
  }
  return dirres;
}

//convert boolean in ImageJ to R string for boolean
function convertBool(bool) {
  if(bool){
    return "TRUE";
  }
  else{
    return "FALSE";
  }
} 

// we progressively construct a R command starting with command0
command0="suppressPackageStartupMessages(library(\"Rsama\"));";


// Interface part
items=newArray("With","Without");
Quality=0;
labell=newArray("None","Treatment And Plate","Plate","Treatment","Filename");

Dialog.create("SAMA-Analyze");
Dialog.addMessage("*Were these parameters analyzed in SAMA-images?");
Dialog.addCheckbox("    Branching", true);
Dialog.addCheckbox("    Lumen", true);
Dialog.addCheckbox("    Thickness", false);

Dialog.addMessage("*Data handling");
Dialog.addCheckbox("        Put data together (only needed once)", true);
Dialog.addCheckbox("        Export sheet (optional)", false);
Dialog.addMessage("*Data analysis");
Dialog.addCheckbox("        Batch analyze treatment effect", true);
Dialog.addCheckbox("        Analyze Reproducibility", true);


Dialog.addMessage("*Choose a subset of the conditions?");
Dialog.addCheckbox("Use interface to choose conditions", false);

Dialog.addMessage("*Options for Analysis");
Dialog.addNumber("Quality Threshold",Quality );
Dialog.addNumber("Size Threshold (volume)",500);
Dialog.addMessage("*Options for Graphs");
Dialog.addChoice("Choose label used in PCA", labell);
Dialog.addCheckbox("Color graphs", true);




Dialog.show();
tree0 = Dialog.getCheckbox();
lumen0 = Dialog.getCheckbox();
bonus0 = Dialog.getCheckbox();

stitchdata = Dialog.getCheckbox();
exportt = Dialog.getCheckbox();
treatment = Dialog.getCheckbox();
consistency = Dialog.getCheckbox();

subcond = Dialog.getCheckbox();

Quality = Dialog.getNumber();
crisize = Dialog.getNumber();
labelr=Dialog.getChoice();
center = false;
colorr = Dialog.getCheckbox();

colorr=convertBool(colorr);
lumen=convertBool(lumen0);
tree=convertBool(tree0);
bonus=convertBool(bonus0);
center=convertBool(center);
chosendir = getDirectory("Choose Data Directory, the folder should be called SAMA-Image data");
dir=File.getParent(chosendir)+"/";
diroutput=createdir(dir,"SAMA-Analyze output/");
Rdatadir =dir+"SAMA-Image data/";
condd="c(\"\")";
nameout="";
filterwith="TRUE";
filter = "";

// start constructing the command streamed to R
if(stitchdata){
  command=command0+"message(\"Putting data together...\");";
  command=command+"mergeF(\""+Rdatadir+"\",lumen="+lumen+",tree="+tree+",bonus="+bonus+");"; 
}else{
  command=command0;
}	


// If the user chooses to select a subset of condition, we build the set of available conditions to display it in the interface. 
if(subcond){
  command=command+"getconditions(\""+Rdatadir+"\",\"external\",versioncounter=4);";	
  res=call("R_bind_sama.execCode",command);
  command=command0;
  open(Rdatadir+"combinedcdt.csv");
  labels= newArray(nResults);
  default=newArray(nResults);
  for (i=0; i<nResults; i++) {
    labels[i]=getResultString("V1",i);
    default[i]=true;
  }
  NN=nResults;
  selectWindow("Results"); 
  run("Close");
  Dialog.create("Choose plotted conditions");
  Dialog.addMessage("*Use filters: ");
  Dialog.addChoice("	Only Treatments", items)
  Dialog.addString("	criterium","", 20);
  Dialog.addMessage("*OR choose manually the conditions to analyze");
  Dialog.addCheckbox("*manual choice?", true);
  Dialog.addCheckboxGroup(NN,1,labels,default);
  Dialog.addString("Prefix to graph filename","custom_conditions", 20);
  Dialog.show();
  
  filterwith=Dialog.getChoice();
  filter = Dialog.getString();
  if(filterwith=="With")
  {filterwith="TRUE";}
  else{filterwith="FALSE";}
  manual=Dialog.getCheckbox();
  vector="c(";
  for (i=0; i<NN; i++) {
    if(Dialog.getCheckbox()){
      vector=vector+"\"" +labels[i]+ "\",";
    }	
  }
  nameout2 = Dialog.getString();
  vector=vector+"\"hahahahaha\")";
  if(manual){
    condd=vector;
    nameout=nameout2;
  }
}   

if(exportt){
  command=command+"message(\"Exporting...\");";
  command=command+"exportF(\""+Rdatadir+"\",\"external\",lumen="+lumen+",tree="+tree+");"; 
}
if(treatment){
  command=command+"message(\"Eating a cookie...\");";
  command=command+"message(\"Comparing treatments...\");";
  command=command+"coarseplotall(\""+Rdatadir+"\","+Quality+",crisize="+crisize+",\"external\",versioncounter=4,colorr="+colorr+",lumen="+lumen+",tree="+tree+",center="+center+",filter=\""+filter+"\",filterwith="+filterwith+",speccond="+condd+",label=\""+labelr+"\",specname=\""+nameout+"\");"; 
}
if(consistency){
  command=command+"message(\"Comparing distributions...\");";
  command=command+"welldisplot(\""+Rdatadir+"\",\"external\",versioncounter=4,colorr="+colorr+",crisize="+crisize+",lumen="+lumen+",tree="+tree+",filter=\""+filter+"\",filterwith="+filterwith+");";
  command=command+"coarseplotall(\""+Rdatadir+"\","+Quality+",crisize="+crisize+",\"external\",versioncounter=4,byplate=T,colorr="+colorr+",lumen="+lumen+",tree="+tree+",center="+center+",filter=\""+filter+"\",filterwith="+filterwith+",speccond="+condd+",label=\""+labelr+"\",specname=\""+nameout+"\");"; 
}

res=call("R_bind_sama.execCode",command);
print("***************************");