#@File   (label = "Source folder", style="directory") sourcePath_File
#@String (label = "Image folder name", value="STITCHED") rawImg_suffix
#@String (label = "Results folder name", value="MAXDISTRIB") results_suffix
#@int    (label = "Transcripts radius (in pixel)", value=2)tx_MaxRadius
#@string (label = "transcripts channel(s)" ) transcripts_channels_str

# balabla
#@string (label = "test", style = "message", value = "value") test

# Author: Benoit Lombardot, Scientific computing facility @ MPI-CBG  
# date: 2015-11-26

##################################################
# import #########################################
from ij import IJ

from mpicbg_scicomp.transcript_analysis import cell_transcript_analysis_v3; # needs Dev version for now

import os
from os import path

#from os import listdir, sep, path, sys;
#from os import makedirs;



##################################################
# get parameters independant of the file #########
IJ.log("===============================\nscript started")

#tx_MaxRadius
transcripts_channels = transcripts_channels_str.split(",")
for i in range(len(transcripts_channels)):
	transcripts_channels[i] = int(transcripts_channels[i])

main_folder= sourcePath_File.getPath(); # base directory containing the raw data and masks folders.
#rawImg_suffix: name of the folder containing the raw image
#results_suffix: name of the folder that will contain the results

rawImgFolder  = path.join(main_folder, rawImg_suffix);
resultFolder = path.join(main_folder, results_suffix) ;
if not path.exists(resultFolder ):
    os.makedirs(resultFolder);


##################################################
# process function ###############################

def process_file(filePath, resultsFolder, filePrefix):
	
	tx_analyzer = cell_transcript_analysis_v3();

	tx_analyzer.setTranscriptMaxRadius(tx_MaxRadius);
	tx_analyzer.setTranscriptChannel(transcripts_channels);
	tx_analyzer.setImagePath(filePath);
	tx_analyzer.setSavePath(resultFolder);
	tx_analyzer.setFilePrefix(filePrefix);
	
	# processing
	imp_aux = IJ.openImage( filePath );
	imp_rawImg = tx_analyzer.convert_input(imp_aux);
	tx_analyzer.save_transcripts_maxima_distribution(imp_rawImg);




############################################################
# main script ##############################################

# select file to analyze
if path.exists(rawImgFolder) :
	rawImg_files_list = [ f for f in os.listdir(rawImgFolder) if ( path.isfile(path.join(rawImgFolder,f)) & (rawImg_suffix in f) )];	

# loop on file to analyze
count= 0;
max_count = len(rawImg_files_list);
for fName in rawImg_files_list :
	
	count = count +1;
	IJ.log("processing file "+fName+" ("+str(count)+"/"+str(max_count)+")")
	fPath      	= path.join(rawImgFolder , fName);
	fNamePrefix    	= fName.split("_"+rawImg_suffix)[0];
	fPathPrefix   = path.join(resultFolder,fNamePrefix);
	
	processed = process_file(fPath, resultFolder, fPathPrefix)
		

IJ.log("script finished\n===============================")