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Move minc pics creation to MRI.pm #149

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Aug 11, 2016
Merged

Move minc pics creation to MRI.pm #149

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a67b807
Move minc pics creation to MRI.pm
gluneau Aug 1, 2016
05d243d
put back row variable
gluneau Aug 2, 2016
cc10400
added $debug and $verbose as parameters
gluneau Aug 10, 2016
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30 changes: 30 additions & 0 deletions uploadNeuroDB/NeuroDB/MRI.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -1200,6 +1200,36 @@ sub make_nii {
$file->setParameter('check_nii_filename', $nifti);
}

=pod
Creates pics associated with MINC files
=cut
sub make_minc_pics {
my ($dbhr, $TarchiveSource, $profile, $minFileID) = @_;
my $where = "WHERE TarchiveSource = ? ";
my $query = "SELECT Min(FileID) AS min, Max(FileID) as max FROM files ";
$query = $query . $where;
my $sth = $${dbhr}->prepare($query);
$sth->execute($TarchiveSource);
print "TarchiveSource is " . $TarchiveSource . "\n";

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@gluneau

I think the print statement was added for debugging purposes (original file did not have it)

my $script = undef;
my $output = undef;
my @row = $sth->fetchrow_array();
if (@row) {
$script = "mass_pic.pl -minFileID $row[$minFileID] -maxFileID $row[1] ".
"-profile $profile";
print "Running mass_pic as follows : " .$script . "\n";

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@gluneau

  1. same comment re. "print" statement
  2. original script had -verbose option appended to the $script command if $verbose is set (you will probably need to pass this variable along with the function call), so it is good to keep this so that it is consistent with what we had before

############################################################
## Note: system call returns the process ID ################
## To get the actual exit value, shift right by eight as ###
## done below ##############################################
############################################################
$output = system($script);
$output = $output >> 8;
}
}

=pod
B<DICOMDateToUnixTimestamp( C<$dicomDate> )>
Converts a DICOM date field (YYYYMMDD) into a unix timestamp
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31 changes: 6 additions & 25 deletions uploadNeuroDB/tarchiveLoader
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Expand Up @@ -486,32 +486,13 @@ if ($valid_study) {
############################################################
############# Create minc-pics #############################
############################################################
print "\nCreating Minc Pics\n" if $verbose;
NeuroDB::MRI::make_minc_pics(\$dbh,
$tarchiveInfo{TarchiveID},
$profile,
0); # minFileID $row[0]
# maxFileID $row[1]

$where = "WHERE TarchiveSource =? ";
$query = "SELECT Min(FileID) AS min, Max(FileID) as max FROM files ";
$query = $query . $where;
if ($debug) {
print $query . "\n";
}
my $sth = $dbh->prepare($query);
$sth->execute($tarchiveInfo{TarchiveID});
my @row = $sth->fetchrow_array();
if (@row) {
my $script = "mass_pic.pl -minFileID $row[0] -maxFileID $row[1] ".
"-profile $profile ";
if ($verbose) {
$script .= " -verbose";
}
############################################################
## Note: system call returns the process ID ################
## To get the actual exit value, shift right by eight as ###
## done below ##############################################
############################################################
$output = system($script);
$output = $output >> 8;

}

############################################################
# spool a new study message ################################
############################################################
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