profileTemplate.pl

=pod
# -----------------------------------------------------------------------------------------------
  WHAT THIS IS:
  Although someone might argue that this is not a config file anymore... this is in fact a config
  WHAT THIS IS FOR:
  For users of the neurodb system... or actually the ones that believe in tarchiving their universe
  WHAT THIS IS NOT:
  A solution for an extant lack of productivity in writing papers
# -----------------------------------------------------------------------------------------------
=cut

=pod
# SECTION I
# -----------------------------------------------------------------------------------------------
  DATABASE settings 
  for database instance you are connecting to
  required: db_name, $db_user, $db_pass, $db_host
# -----------------------------------------------------------------------------------------------
=cut

@db = ('DBNAME','DBUSER', 'DBPASS', 'DBHOST');


=pod
# SECTION II
# -----------------------------------------------------------------------------------------------
  custom settings
  these functions are very specific for any given study. Using them seems to be the only way of
  having one system that rules them all...
# -----------------------------------------------------------------------------------------------
=cut

# extracts the subject and timepoint identifiers from the patient name 
# assumes identifers are stored as <PSCID>_<DCCID>_<visit> in PatientName field, where <visit> is 3 digits.
sub getSubjectIDs {
    my ($patientName, $patientID, $scannerID, $dbhr, $db) = @_;

    my %subjectID; # Will stored subject IDs.
    
     # If patientName is phantom scan or test scan
     # CandID is scanner DCCID (based on site alias)
     # visitLabel is scan patient name
     # Set createVisitLable to 
     #      a. 1 if imaging pipeline should create the visit label (when visit label has not been created yet in the database. 
     #      b. 0 if imaging pipeline should not create the visit label (when visit label has not been created yet in the database. 
    if ($patientName =~ /PHA/i or $patientName =~ /TEST/i) {

        $subjectID{'CandID'}    = NeuroDB::MRI::my_trim(NeuroDB::MRI::getScannerCandID($scannerID, $db));
        $subjectID{'visitLabel'}= NeuroDB::MRI::my_trim($patientName);
        $subjectID{'createVisitLabel'} = 1; 

     # If patient match PSCID_DCCID_VisitLabel
     # Determine PSCID, DCCID and visitLabel based on patient name
    } elsif ($patientName =~ /([^_]+)_(\d+)_([^_]+)/) {

        $subjectID{'PSCID'}         = NeuroDB::MRI::my_trim($1);
        $subjectID{'CandID'}        = NeuroDB::MRI::my_trim($2);
        $subjectID{'visitLabel'}    = NeuroDB::MRI::my_trim($3);
        $subjectID{'createVisitLabel'} = 0; 

        # Note, this function will ensure that the PSCID/CandID information refers to a valid candidate
        # and it will check that the Visit label exists in the Visit_Windows table
        if(!NeuroDB::MRI::subjectIDIsValid($subjectID{'CandID'}, $subjectID{'PSCID'}, $subjectID{'visitLabel'}, $dbhr)) {
            return undef;
        }

        print "PSCID is: "            . $subjectID{'PSCID'}      . 
                "\n CandID id: "      . $subjectID{'CandID'}     . 
                "\n visit_label is: " . $subjectID{'visitLabel'} . "\n";

    }
   
    # Return subjectIDs
    return \%subjectID;
}

# determines if a given subjectID is a phantom or not
# returns 1 if a phantom, 0 for non-phantom
sub isPhantom {
    my $subjectIDref = shift;
    if($subjectIDref->{'PSCID'} =~ /PHA/i) {
        return 1;
    }
    return 0;
}

# ----------- OPTIONAL SUBROUTINE
# This function allows the user to decide which images are to be inserted into the database.
# The current default setting is to allow insertion of all the scans
# that meet an mri_protocol table entry to be inserted;
# this is achieved by returning 1 when $acquisitionProtocol ne 'unknown'.
# Alternatively, this routine can be tailored to the user's needs; it can be made to
# insert scans based on exact (eq 't1') or partial regex matching (=~ /despot/), or case 
# insensitive partial matching to the scan type (=~ /dti/i), etc... 
# as shown in the commented-out line below.
sub isFileToBeRegisteredGivenProtocol {
    my $acquisitionProtocol = shift;
    if($acquisitionProtocol ne 'unknown') {
#    if($acquisitionProtocol eq 't1' or $acquisitionProtocol eq 't2' or $acquisitionProtocol eq 'pd' or $acquisitionProtocol eq 'mrs' or $acquisitionProtocol=~ /dti/i or $acquisitionProtocol =~ /despot/) {
        return 1;
    }
    return 0;
}

# ----------- OPTIONAL SUBROUTINE
# Fetch CandID and Visit info from DTI folder.
sub  get_DTI_CandID_Visit {
    my ($native_dir) =   @_;

    if  ($native_dir =~  /assembly\/(\d\d\d\d\d\d)\/(V\d{1,2})\/mri\//i)  {  
        my  $subjID =   $1;
        my  $visit  =   $2;
        return  ($subjID,$visit);
    }else{
        return  undef;
    }
}