/* 
 * Skyscan Importer
 * Script to import from .log file & prepare for analysis
 * Matt Foley, SMM, USYD
 * Version 0.1b (Beta)
 * 2018-03-06
 */


var PixelSize;
var FileName;
var FirstSection;
var FileType;
var ReconCheck;

macro "Import Skyscan Dataset" {

dir = getDirectory("Choose Directory containing Log File");
extension = ".log";
  processFolder(dir);


///////////////////////////////////////////////////// FUNCTIONS

  function processFolder(dir) 	{
     list = getFileList(dir);
     for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              processFolder(dir+list[i]);
          else if (endsWith(list[i], extension))
             {processImage(dir, list[i]);
	if(ReconCheck==true)
	{
	 if (getBoolean("Do you want to continue loading file\n"+FileName+"\nWith pixel size: "+PixelSize+"um\n \n"+dir+list[i]+"")) 
	        { 
	ImportSkyscan(dir,FileName,FirstSection, FileType);
	       
	getDimensions(width,height,channels,slices,frames);
	run("Properties...", "channels="+channels+" slices="+slices+" frames="+frames+" unit=um pixel_width="+PixelSize+" pixel_height="+PixelSize+" voxel_depth="+PixelSize+"");
			 }
	}
	             }
	             
	      								}
  								}

  function processImage(dir, name) {
	filestring=File.openAsString(dir+name); 
	rows=split(filestring, "\n"); 


	
	Variable=newArray(); 
	Value=newArray(); 
	Variable = fn_PadArray(Variable, rows.length+1);
	Value = fn_PadArray(Value, rows.length+1);
	ReconCheck = false;




	Variable[0]		= "Data location:";
	Value[0]		= dir+name;	

	for(i=0; i<rows.length; i++)	{ 
		if(indexOf(rows[i], "=")<0)
					{Variable[i+1]=rows[i]; 
					Value[i+1]="";
					if(startsWith(rows[i], "[Reconstruction]")==1){
						ReconCheck = true;
							}
					} 
			else{
					columns=split(rows[i],"="); 
					Variable[i+1]=columns[0];
					Value[i+1]=columns[1]; 
					
					
					// Extracting usefulness
					if(startsWith(columns[0], "Image Pixel Size")==1){
						PixelSize = parseFloat(columns[1]);
						}
					if(startsWith(columns[0], "Filename Prefix")==1){
						FileName = columns[1];
						}
					if(startsWith(columns[0], "First Section")==1){
						FirstSection = columns[1];
						}
					if(startsWith(columns[0], "Result File Type")==1){
						FileType = columns[1];
						}

	
				} 
									}
						
	Array.show("Import", Variable,Value);
								}

function pad (a, left) { 
while (lengthOf(""+a)<left) a="0"+a; 
return ""+a; 
} 

function ImportSkyscan(dir,FileName,FirstSection, FileType)
{
run("Image Sequence...", "open=["+dir+FileName+pad(FirstSection,4)+"."+FileType+"] file=((?i)[a-z0-9].(?i)"+FileType+") sort");
}


}

function fn_PadArray(array, n){
	for(j=0; j<n; j++)
	{array = Array.concat(array, 0);
	}
	return array;
}