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#!/usr/bin/env perl
use strict; use warnings;
use feature 'say';

use Pod::Usage;
use Getopt::Long;
use feature 'say';
use App::AFNI::SiemensPhysio;

=head1 NAME

siemphysdat - chop Siemens Physiologic Monitoring Unit (PMU) physio files to MR timing for AFNI's retroTS


=head1 SYNOPSIS


 siemphysdat [options] phsyiofile1 physiofile2 MRdir/

Options:

  -s [alt+z],alt-z,seq+z,               # slice order
     seq-z,filename 

  -o prefix                             # where to save files,
                                        # trailing slash are important

  -r [matlab]|McRetroTs|                # retoTS method
     show    | none 

  -t [none],MR,Phys,all                 # trust times&samplerate
                                        # dont compare to index count


C<-r none> is useful if you only want the *dat files

C<-t MR> is useful for testing against data/

C<-t Phys> is useful for forcing a sampling rate

=head1 OUTPUT

=over

=item C<*dat> 

chopped volrage meassurements with triggers removed, 

=item C<*slibase.1D> 

RVT from AFNI's RetroTS ready for C<afni_proc.py> or C<3dretroicor>

=back



=head1 DESCRIPTION

=begin html

<img src="https://raw.githubusercontent.com/LabNeuroCogDevel/siemphysdat/master/icon.png"></img>

=end html

B<siemphysdat> will chop two physio files given timing of DICOMS in MRdir and save in a format RetroTS.m likes.


=head2 SEE ALSO

App::AFNI::SiemensPhysio

=cut




# read in arguments
my $type      ='matlab';
my $oprefix   ='';
my $sliceOrder='alt+z';
my $trustIdx='none';

GetOptions('retrotype:s'=>\$type, 
           'oprefix:s'=>\$oprefix,
           'sliceOrder:s'=>\$sliceOrder,
           'trustIdx:s'=>\$trustIdx,
           ) or pod2usage(1);

# now that we've removed the options
# check for inputs
pod2usage(1) if $#ARGV<2;
for (@ARGV) { die "cannot read  '$_', should be physio file or MR dir:" if ! -r $_ }
my ($pfile1,$pfile2,@MRs) = @ARGV;


# intialize object
my $p = App::AFNI::SiemensPhysio->new({
          VERB=>1,
          sliceOrder=>$sliceOrder, 
          prefix=>$oprefix, 
          trustIdx=>$trustIdx