#!/usr/bin/env perl
#
# generate tal reg image using avg,std,input,output
#
# Copyright Alan C. Evans
# Professor of Neurology
# McGill University
#


use strict;
use warnings "all";
use File::Basename;

# Takes surface volume outside_val inside_val error.mnc

my $surface_obj = $ARGV[0];
my $volume_data = $ARGV[1];
my $inside_val= $ARGV[2];
my $outside_val = $ARGV[3];
my $error_mnc = $ARGV[4];

my $temp_scanned =  "${error_mnc}_temp1.mnc";
my $temp_msdmask =  "${error_mnc}_temp2.mnc";
my $temp_scanned_blurred =  "${error_mnc}_temp3.mnc";
my $inner_mask=  "${error_mnc}_temp4.mnc"; 
my $outer_mask   =  "${error_mnc}_temp5.mnc" ;
my $combined_raw    =  "${error_mnc}_temp6.mnc";


#create a single line of surface in 3D vol
my @args = ("scan_object_to_volume",$volume_data,$surface_obj,$temp_scanned);
#print @args;
system(@args)== 0 or die "system @args failed: $?";

#Create a mask which includes the surface 1 inside, 0 outside
@args = ("msd_masks","-clobber",$volume_data,$surface_obj,$temp_msdmask);
#print @args;
system(@args) == 0 or die "system @args failed: $?";

#blur the single line to create a roi 2mm from the scanned surface object.
@args = ("mincblur","-clobber","-fwhm","2",$temp_scanned,$temp_scanned_blurred);
#print @args;
system(@args) == 0 or die "system @args failed: $?";

$temp_scanned_blurred = "${temp_scanned_blurred}_blur.mnc";

#create the inner mask
 @args = ("minccalc","-clobber","-expr", "if(A[0]>0&&A[1]>0.5&&A[2]<0.5){out=1;}else{out=0;}", $temp_scanned_blurred,$temp_msdmask,$temp_scanned,$inner_mask);
#print @args;
system(@args) == 0 or die "system @args failed: $?";
 
#create the outer mask
 @args = ("minccalc","-clobber","-expr","if (A[0]>0 &&A[1]<0.5){out=1;}else{out=0;}",$temp_scanned_blurred,$temp_msdmask,$outer_mask);
#print @args;
system(@args) == 0 or die "system @args failed: $?";

# create the bad voxels  gray inside or white outside
@args = ("minccalc","-clobber","-expr","if((A[0]>0.5 &&abs(A[2]-${outside_val})<0.5)||(A[1]>0.5 &&abs(A[2]-${inside_val})<0.5)){out=1;}else{out=0;}" ,$inner_mask,$outer_mask,$volume_data,$combined_raw);
#print @args;
system(@args) == 0 or die "system @args failed: $?";

#blur a bit to focus our attention...
 @args = ("mincblur","-clobber","-fwhm","2",$combined_raw,$error_mnc);
#print @args;
system(@args) == 0 or die "system @args failed: $?";

@args = ("mv", "${error_mnc}_blur.mnc", $error_mnc);
 system(@args) == 0 or die "system @args failed: $?";
#get rid of all the crap...
 @args = ("rm",$temp_scanned,$temp_msdmask , $temp_scanned_blurred,$inner_mask, $outer_mask,$combined_raw);
#print @args;
system(@args) == 0 or die "system @args failed: $?";