App-AFNI-SiemensPhysio

 view release on metacpan or  search on metacpan

lib/App/AFNI/SiemensPhysio.pm  view on Meta::CPAN

   
   # reset rate if its only off by a very small amount
   # and we don't trust the sample rate we provided
   my $newrate = abs($self->{physStart}- $self->{physEnd})/$#{$self->{measures}};
   $self->{PhRate} = $newrate 
     if abs($newrate-$self->{PhRate}) < .00001  and
        $self->{trustIdx}!~/All|Phys/i;


   say "file is $self->{ptype} with $#{$self->{measures}} samples, " ,
       "$self->{physStart}s - $self->{physEnd}s, ",
       "sample rate adjusted to $self->{PhRate}"
     if $self->{VERB};

   # does the time match the sample rate and number of samples
   timeCheck($self->{physStart},
             $self->{physEnd},
             $#{$self->{measures}},
             $self->{PhRate} ) unless $self->{trustIdx}=~/All|Phys/i;
}

lib/App/AFNI/SiemensPhysio.pm  view on Meta::CPAN

 my $ATidx= getidx('AcqTime');

 # find max and min acq time from all MR*s
 my ($starttime, $endtime) = minmax( map {$_->[$ATidx] } @v);


 ## set start and end
 $self->{MRstart} = getMRAcqSecs($starttime);
 $self->{MRend}   = getMRAcqSecs($endtime);

 say "MR starts $self->{MRstart} (DICOM $starttime) and ends $self->{MRend} (DICOM $endtime)"
   if $self->{VERB};

 timeCheck($self->{MRstart},
           $self->{MRend},
           $self->{nDcms},
           $self->{TR}) unless $self->{trustIdx}=~/All|MR/i;
}

=head2 writeMRPhys

lib/App/AFNI/SiemensPhysio.pm  view on Meta::CPAN

   # get dir
   my $bn=dirname($self->{prefix});
   croak "prefix directory ($bn) does not exist!" if ! -d $bn;
   $outfile=$self->{prefix}.$outfile;
 }

 $self->{dat}->{$self->{ptype}}=$outfile;

 my @pvals = $self->getMRPhys;

 say "saving to $outfile" if $self->{VERB};
 writeDat($outfile,@pvals)
}




=head2 retroTS

This is kludgy code hacked together and untested :)
=over

lib/App/AFNI/SiemensPhysio.pm  view on Meta::CPAN

   "Opts.Cardfile"   => "'".$self->{dat}->{puls}."'", # Cardiac data file
   "Opts.PhysFS"     => 1/$self->{PhRate},    # Physioliogical signal sampling frequency in Hz.
   "Opts.Nslices"    => $self->{nslice},      # Number of slices
   "Opts.VolTR"      => $self->{TR},          # Volume TR in seconds
   "Opts.SliceOrder" => "'".$self->{sliceOrder}."'"  # ['alt+z']/'alt-z'/'seq+z'/'seq-z'/'Custom'/filename.1D
 );

 # McRetroTS Respdatafile ECGdatafile VolTR Nslices SamplingFreq(PhysFS) ShowGraphs
 my @mcrts = qw/Opts.Respfile Opts.Cardfile Opts.VolTR Opts.Nslices Opts.PhysFS/;
 my $mccmd =  "McRetroTs @params{@mcrts}";
 say $mccmd if $runtype !~ /matlab|McRetroTs/g ;;


 # if have matlab and singal toolbox, can use this
 my $cmd = join("; ", map { join("=",$_,$params{$_}) } keys %params);
 $cmd .= "; Opts.ShowGraphs=0;Opts.Quiet=0;"; # turn off graphs, turn on verbose
 $cmd .= " rts = RetroTS(Opts)";

 # we should wrap matlab up in a try+quit so we dont hang in ML command window on a failure
 my $matlabwrap= qq/$matlabbin -nodisplay -r "try; $cmd; catch err; err, exit(1); end; rts, quit;"/;

 say $matlabwrap if $runtype !~ /matlab|McRetroTs/i;
 # eg
 # matlab -nodisplay -r "try; Opts.Cardfile='rest_164627.359000.puls.dat'; Opts.VolTR=1.5; Opts.Nslices=29; Opts.SliceOrder='alt+z'; Opts.PhysFS=50.0074711455304; Opts.Respfile='rest_164627.359000.resp.dat'; rts = RetroTS(Opts); catch; exit(666); end...

 # with either command, the original output name will be "oba.slibase.1D"
 # change that to our basename (assume resp and puls have same basename, use one from resp)
 my $outputname = $self->{dat}->{resp};
 $outputname =~ s/.resp.dat$/.slibase.1D/;
 
 # or rename to specified input
 #my $outputname=shift if $#_;

lib/App/AFNI/SiemensPhysio.pm  view on Meta::CPAN

## print whats up
sub sayIndex {
 my $self=shift;

 # print out start and stop index for ps and pe
 my $ps = timeToSamples($self->{physStart},$self->{physStart},$self->{PhRate});
 my $pe = timeToSamples($self->{physStart},$self->{physEnd},$self->{PhRate});
 my $s  = $self->{MRstartIdx} || undef;
 my $e  = $self->{MRendIdx}   || undef;
 # lets talk about what we have
 say "(ps  ) $self->{physStart}  | MR $self->{MRstart} $self->{MRend} | $self->{physEnd} (pe)  ";
 say "(sidx) $ps          | MR $s  $e     | $pe   (eidx)" if $s and $e;

}



1;