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MRI.pm
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MRI.pm
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package NeuroDB::MRI;
=pod
=head1 NAME
NeuroDB::MRI -- A set of utility functions for performing common tasks
relating to MRI data (particularly with regards to registering MRI
files into the LORIS system)
=head1 SYNOPSIS
use NeuroDB::File;
use NeuroDB::MRI;
use NeuroDB::DBI;
my $dbh = NeuroDB::DBI::connect_to_db();
my $file = NeuroDB::File->new(\$dbh);
$file->loadFileFromDisk('/path/to/some/file');
$file->setFileData('CoordinateSpace', 'nonlinear');
$file->setParameter('patient_name', 'Larry Wall');
my $parameterTypeID = $file->getParameterTypeID('patient_name');
my $parameterTypeCategoryID = $file->getParameterTypeCategoryID('MRI Header');
=head1 DESCRIPTION
Really a mishmash of utility functions, primarily used by C<process_uploads> and
all of its children.
=head2 Methods
=cut
use Exporter();
use Math::Round;
use Time::JulianDay;
use File::Temp qw(tempdir);
use File::Basename;
use Data::Dumper;
use Carp;
use Time::Local;
use FindBin;
use DICOM::DICOM;
use NeuroDB::objectBroker::MriScanTypeOB;
use NeuroDB::objectBroker::MriScannerOB;
use NeuroDB::objectBroker::PSCOB;
use NeuroDB::UnexpectedValueException;
use NeuroDB::Notify;
$VERSION = 0.2;
@ISA = qw(Exporter);
# Number of decimals considered when testing if two floats are equal
$FLOAT_EQUALS_NB_DECIMALS = 4;
@EXPORT = qw();
@EXPORT_OK = qw(identify_scan in_range get_headers get_info get_ids get_objective identify_scan_db scan_type_text_to_id scan_type_id_to_text register_db get_header_hash get_scanner_id get_psc compute_hash is_unique_hash make_pics select_volume);
=pod
=head3 subjectIDExists($ID_type, ID_value, $dbhr)
Verifies that the subject ID (C<CandID> or C<PSCID>) exists.
INPUTS:
- $ID_type : type of candidate ID (C<CandID> or C<PSCID>)
- $ID_value: value of the candidate ID
- $dbhr : the database handle reference
RETURNS: 1 if the ID exists in the candidate table, 0 otherwise
=cut
sub subjectIDExists {
my ($ID_type, $ID_value, $dbhr) = @_;
# check if ID already exists in the candidate table
my $query = "SELECT COUNT(*) AS idExists FROM candidate WHERE $ID_type=?";
my $sth = $${dbhr}->prepare($query);
$sth->execute($ID_value);
my $rowhd = $sth->fetchrow_hashref();
return $rowhd->{'idExists'} > 0;
}
=pod
=head3 getScannerCandID($scannerID, $db)
Retrieves the candidate (C<CandID>) for the given scanner.
INPUTS: the scanner ID and the database object
RETURNS: the C<CandID> or (if none exists) undef
=cut
sub getScannerCandID {
my ($scannerID, $db) = @_;
my $mriScannerOB =
NeuroDB::objectBroker::MriScannerOB->new(db => $db);
my $resultRef = $mriScannerOB->get({ID => $scannerID});
return @$resultRef ? $resultRef->[0]->{'CandID'} : undef;
}
=pod
=head3 getSessionInformation($subjectIDref, $studyDate, $dbh, $db)
Gets information for the session with the given CandID and visitLabel
(contained inside the hashref C<$subjectIDref>). If no such session
exists, the method will try to create it using the supplied parameters.
INPUTS:
- $subjectIDref: hash reference of subject IDs
- $studyDate : study date
- $dbh : database handle
- $db : database object
RETURNS: an array of 2 elements:
- A reference to a hash containing the session properties:
C<ID> => session ID.
C<ProjectID> => project ID for the session.
C<SubprojectID> => sub-project ID for the session.
C<CandID> => candidate ID for the session.
C<Visit_label> => session visit label.
The reference will be C<undef> if the session cannot be retrieved/created.
- An error message (C<''> if no errors occured while retrieving/creating the session)
=cut
sub getSessionInformation {
my ($subjectIDref, $studyDate, $dbh, $db) = @_;
my ($sessionID, $studyDateJD);
my ($query, $sth);
# find a matching timepoint
$query = "SELECT ID, ProjectID, SubprojectID, CandID, Visit_label "
. "FROM session "
. "WHERE CandID=? "
. "AND LOWER(Visit_label)=LOWER(?) "
. "AND Active='Y'";
$sth = $dbh->prepare($query);
$sth->execute($subjectIDref->{'CandID'}, $subjectIDref->{'visitLabel'});
##### if it finds an existing session it does this:
if($sth->rows > 0) {
my $timepoint = $sth->fetchrow_hashref();
my %session = (
ID => $timepoint->{'ID'},
ProjectID => $timepoint->{'ProjectID'},
SubprojectID => $timepoint->{'SubprojectID'},
CandID => $timepoint->{'CandID'},
Visit_label => $timepoint->{'Visit_label'},
);
$sth->finish();
return (\%session, '');
}
if (!$subjectIDref->{'createVisitLabel'}) {
my $msg = sprintf(
"Visit %s for candidate %d does not exist.",
$subjectIDref->{'visitLabel'},
$subjectIDref->{'CandID'}
);
return (undef, $msg);
}
# Since we'll be creating a visit, ensure that the subprojectID and ProjectID
# have been defined in the profile file
if (!defined $subjectIDref->{'SubprojectID'}) {
return (undef, "Cannot create visit: profile file does not define the visit's SubprojectID");
}
if (!defined $subjectIDref->{'ProjectID'}) {
return (undef, "Cannot create visit: profile file does not define the visit's ProjectID");
}
# Ensure relationship between ProjectID and SubprojectID is legit
# according to project_subproject_rel. This also validates the existence
# of ProjectID and SubprojectID in tables Project and subproject respectively.
$query = "SELECT ProjectID, SubprojectID "
. "FROM project_subproject_rel "
. "WHERE ProjectID=? "
. "AND SubprojectID=?";
$sth = $dbh->prepare($query);
$sth->execute($subjectIDref->{'ProjectID'}, $subjectIDref->{'SubprojectID'});
# If there's no entry in project_subproject_rel for (ProjectID, SubprojectID)
if ($sth->rows == 0) {
my $msg = sprintf(
"Cannot create visit with project ID %d and sub-project ID %d: no such association in table %s",
$subjectIDref->{'ProjectID'},
$subjectIDref->{'SubprojectID'},
'project_subproject_rel'
);
return (undef, $msg);
}
# determine the visit number and centerID for the next session
my $newVisitNo = 0;
my $centerID = 0;
if($subjectIDref->{'isPhantom'}) {
# calibration data (PHANTOM_site_date | LIVING_PHANTOM_site_date | *test*)
my @pscInfo = getPSC($subjectIDref->{'visitLabel'}, $dbhr, $db);
$centerID = $pscInfo[1];
}
# determine the centerID and new visit number (which is now deprecated) if getPSC() failed.
if($centerID == 0) {
$query = "SELECT IFNULL(MAX(VisitNo), 0)+1 AS newVisitNo, CenterID "
. "FROM session "
. "WHERE CandID = ? "
. "GROUP BY CandID, CenterID";
$sth = $dbh->prepare($query);
$sth->execute($subjectIDref->{'CandID'});
if($sth->rows > 0) {
my $rowref = $sth->fetchrow_hashref();
$newVisitNo = $rowref->{'newVisitNo'};
$centerID = $rowref->{'CenterID'};
# fixme add some debug messages if this is to be kept
print "Set newVisitNo = $newVisitNo and centerID = $centerID\n";
} else {
$query = "SELECT RegistrationCenterID AS CenterID FROM candidate "
. "WHERE CandID=" . $dbh->quote($subjectIDref->{'CandID'});
$sth = $dbh->prepare($query);
$sth->execute();
if($sth->rows > 0) {
my $rowref = $sth->fetchrow_hashref();
$centerID = $rowref->{'CenterID'};
print "Set centerID = $centerID\n";
} else {
$centerID = 0;
print "No centerID\n";
}
}
}
$newVisitNo = 1 unless $newVisitNo;
$centerID = 0 unless $centerID;
# Insert the new session setting Current_stage to 'Not started' because that column is important
# to the behavioural data entry gui.
$query = "INSERT INTO session "
. "SET CandID = ?, "
. " Visit_label = ?, "
. " CenterID = ?, "
. " VisitNo = ?, "
. " Current_stage = 'Not Started', "
. " Scan_done = 'Y', "
. " Submitted = 'N', "
. " SubprojectID = ?, "
. " ProjectID = ?";
$dbh->do(
$query, undef,
$subjectIDref->{'CandID'},
$subjectIDref->{'visitLabel'},
$centerID,
$newVisitNo,
$subjectIDref->{'SubprojectID'},
$subjectIDref->{'ProjectID'}
);
$sessionID = $dbh->{'mysql_insertid'}; # retain id of inserted row
my %session = (
ID => $sessionID,
ProjectID => $subjectIDref->{'ProjectID'},
SubprojectID => $subjectIDref->{'SubprojectID'},
Visit_label => $subjectIDref->{'visitLabel'},
CandID => $subjectIDref->{'CandID'}
);
return (\%session, '');
}
=pod
=head3 identify_scan_db($psc, $subjectref, $tarchiveInfoRef, $fileref, $dbhr, $db, $minc_location, $uploadID)
Determines the type of the scan described by MINC headers based on
C<mri_protocol> table in the database.
INPUTS:
- $psc : center's name
- $subjectref : reference on the hash that contains the subject information
- $tarchiveInfoRef: reference on the tarchive
- $fileref : file hash ref
- $dbhr : database handle reference
- $db : database object
- $minc_location : location of the MINC files
- $uploadID : ID of the upload containing the scan
RETURNS: textual name of scan type from the C<mri_scan_type> table
=cut
sub identify_scan_db {
my ($psc, $subjectref, $tarchiveInfoRef, $fileref, $dbhr, $db, $minc_location, $uploadID) = @_;
my $candid = ${subjectref}->{'CandID'};
my $pscid = ${subjectref}->{'PSCID'};
my $visitLabel = ${subjectref}->{'visitLabel'};
my $projectID = ${subjectref}->{'ProjectID'};
my $subprojectID = ${subjectref}->{'SubprojectID'};
my $tarchiveID = $tarchiveInfoRef->{'TarchiveID'};
# get parameters from minc header
my $patient_name = ${fileref}->getParameter('patient_name');
my $xstep = ${fileref}->getParameter('xstep');
my $ystep = ${fileref}->getParameter('ystep');
my $zstep = ${fileref}->getParameter('zstep');
my $xspace = ${fileref}->getParameter('xspace');
my $yspace = ${fileref}->getParameter('yspace');
my $zspace = ${fileref}->getParameter('zspace');
my $slice_thickness = ${fileref}->getParameter('slice_thickness');
my $seriesUID = ${fileref}->getParameter('series_instance_uid');
my $series_description = ${fileref}->getParameter('series_description');
my $image_type = ${fileref}->getParameter('acquisition:image_type');
my $mriProtocolGroupID;
# get parameters specific to MRIs
my ($tr, $te, $ti, $time);
if ($fileref->{parameters}{modality} eq "MR") {
$tr = ${fileref}->getParameter('repetition_time');
$te = ${fileref}->getParameter('echo_time');
$ti = ${fileref}->getParameter('inversion_time');
if (defined($tr)) { $tr = &Math::Round::nearest(0.01, $tr*1000); }
if (defined($te)) { $te = &Math::Round::nearest(0.01, $te*1000); }
if (defined($ti)) { $ti = &Math::Round::nearest(0.01, $ti*1000); }
$time = ${fileref}->getParameter('time');
} elsif ($fileref->{parameters}{modality} eq "PT") {
# Place to add stuff specific to PET images
}
if(0) {
if ($fileref->{parameters}{modality} eq "MR") {
print "\ntr:\t$tr\nte:\t$te\nti:\t$ti\nst:\t$slice_thickness\n";
}
print "time;\t$time\n";
print "xspace:\t$xspace\nyspace:\t$yspace\nzspace:\t$zspace\n";
print "xstep:\t$xstep\nystep:\t$ystep\nzstep:\t$zstep\n";
}
# compute n_slices from DIMnele's
my $n_slices = 0;
# get ScannerID from DB
my $mriScannerOB = NeuroDB::objectBroker::MriScannerOB->new( db => $db );
my $resultsRef = $mriScannerOB->get( {
Manufacturer => $fileref->getParameter('manufacturer'),
Model => $fileref->getParameter('manufacturer_model_name'),
Serial_number => $fileref->getParameter('device_serial_number'),
Software => $fileref->getParameter('software_versions')
});
# default ScannerID to 0 if we have no better clue.
my $ScannerID = @$resultsRef> 0 ? $resultsRef->[0]->{'ID'} : 0;
#===========================================================#
# Get the list of lines in the mri_protocol table that #
# apply to the given scan based on the center name #
#===========================================================#
$query = "SELECT *
FROM mri_protocol
JOIN mri_protocol_group_target mpgt USING (MriProtocolGroupID)
WHERE (
(Center_name = ? AND ScannerID = ?)
OR ((Center_name='ZZZZ' OR Center_name='AAAA') AND ScannerID='0'))";
#============================================================#
# Add to the query the clause related to the Project ID, the #
# subproject ID and visit label. #
#============================================================#
$query .= defined $projectID
? ' AND (mpgt.ProjectID IS NULL OR mpgt.ProjectID = ?)'
: ' AND mpgt.ProjectID IS NULL';
$query .= defined $subprojectID
? ' AND (mpgt.SubprojectID IS NULL OR mpgt.SubprojectID = ?)'
: ' AND mpgt.SubprojectID IS NULL';
$query .= defined $visitLabel
? ' AND (mpgt.Visit_label IS NULL OR mpgt.Visit_label = ?)'
: ' AND mpgt.Visit_label IS NULL';
$query .= ' ORDER BY Center_name ASC, ScannerID DESC';
my @bindValues = ($psc, $ScannerID);
push(@bindValues, $projectID) if defined $projectID;
push(@bindValues, $subprojectID) if defined $subprojectID;
push(@bindValues, $visitLabel) if defined $visitLabel;
$sth = $${dbhr}->prepare($query);
$sth->execute(@bindValues);
my @rows = @{ $sth->fetchall_arrayref({}) };
# If no lines in the mri_protocol_group_target matches the ProjectID/SubprojectID/VisitLabel
# then no lines of the mri_protocol table can be used to identify the scan type. This is most
# likely a setup issue: mri_protocol/mri_protocol_group/mri_protocol_group_target do not cover
# all the cases. Warn.
if(@rows == 0) {
my $msg = "Warning! No protocol group can be used to determine the scan type "
. "of $minc_location.\nIncorrect/incomplete setup of table mri_protocol_group_target: "
. " setting scan type to 'unknown'";
print "$msg\n";
my $notify = NeuroDB::Notify->new( $dbhr );
$notify->spool('mri upload processing class', $msg, 0, 'MRI.pm', $uploadID, 'N', 'Y');
} else {
# If more than one line in the mri_protocol_group_target matches the ProjectID/SubprojectID/VisitLabel
# then table mri_protocol_group_target was not setup properly. Warn.
my %mriProtocolGroupIDs = map { $_->{'MriProtocolGroupID'} => 1 } @rows;
if(keys %mriProtocolGroupIDs > 1) {
my $msg = "Warning! More than one protocol group can be used to identify the scan type of $minc_location\n"
. "Ambiguous setup of table mri_protocol_group_target: setting scan type to 'unknown'";
print "$msg\n";
my $notify = NeuroDB::Notify->new( $dbhr );
$notify->spool('mri upload processing class', $msg, 0, 'MRI.pm', $uploadID, 'N', 'Y');
} else {
$mriProtocolGroupID = [ keys %mriProtocolGroupIDs ]->[0];
# check against all possible scan types
foreach my $rowref (@rows) {
my $sd_regex = $rowref->{'series_description_regex'};
my $tr_min = $rowref->{'TR_min'};
my $tr_max = $rowref->{'TR_max'};
my $te_min = $rowref->{'TE_min'};
my $te_max = $rowref->{'TE_max'};
my $ti_min = $rowref->{'TI_min'};
my $ti_max = $rowref->{'TI_max'};
my $xspace_min = $rowref->{'xspace_min'};
my $xspace_max = $rowref->{'xspace_max'};
my $yspace_min = $rowref->{'yspace_min'};
my $yspace_max = $rowref->{'yspace_max'};
my $zspace_min = $rowref->{'zspace_min'};
my $zspace_max = $rowref->{'zspace_max'};
my $xstep_min = $rowref->{'xstep_min'};
my $xstep_max = $rowref->{'xstep_max'};
my $ystep_min = $rowref->{'ystep_min'};
my $ystep_max = $rowref->{'ystep_max'};
my $zstep_min = $rowref->{'zstep_min'};
my $zstep_max = $rowref->{'zstep_max'};
my $time_min = $rowref->{'time_min'};
my $time_max = $rowref->{'time_max'};
my $slice_thick_min = $rowref->{'slice_thickness_min'};
my $slice_thick_max = $rowref->{'slice_thickness_max'};
if(0) {
print "\tChecking ".&scan_type_id_to_text($rowref->{'Scan_type'}, $db)." ($rowref->{'Scan_type'}) ($series_description =~ $sd_regex)\n";
print "\t";
if($sd_regex && ($series_description =~ /$sd_regex/i)) {
print "series_description\t";
}
print &in_range($tr, "$tr_min-$tr_max") ? "TR\t" : '';
print &in_range($te, "$te_min-$te_max") ? "TE\t" : '';
print &in_range($ti, "$ti_min-$ti_max") ? "TI\t" : '';
print &in_range($xspace, "$xspace_min-$xspace_max") ? "xspace\t" : '';
print &in_range($yspace, "$yspace_min-$yspace_max") ? "yspace\t" : '';
print &in_range($zspace, "$zspace_min-$zspace_max") ? "zspace\t" : '';
print &in_range($xstep, "$xstep_min-$xstep_max") ? "xstep\t" : '';
print &in_range($ystep, "$ystep_min-$ystep_max") ? "ystep\t" : '';
print &in_range($zstep, "$zstep_min-$zstep_max") ? "zstep\t" : '';
print &in_range($time, "$time_min-$time_max") ? "time\t" : '';
print &in_range($slice_thickness, "$slice_thick_min-$slice_thick_max") ? "ST\t" : '';
print "\n";
}
if ($sd_regex) {
if ($series_description =~ /$sd_regex/i) {
return &scan_type_id_to_text($rowref->{'Scan_type'}, $db);
}
} else {
if ( &in_range($tr, "$tr_min-$tr_max" )
&& &in_range($te, "$te_min-$te_max" )
&& &in_range($ti, "$ti_min-$ti_max" )
&& &in_range($xspace, "$xspace_min-$xspace_max" )
&& &in_range($yspace, "$yspace_min-$yspace_max" )
&& &in_range($zspace, "$zspace_min-$zspace_max" )
&& &in_range($xstep, "$xstep_min-$xstep_max" )
&& &in_range($ystep, "$ystep_min-$ystep_max" )
&& &in_range($zstep, "$zstep_min-$zstep_max" )
&& &in_range($time, "$time_min-$time_max" )
&& &in_range($slice_thickness, "$slice_thick_min-$slice_thick_max")
&& (!$rowref->{'image_type'} || $image_type =~ /\Q$rowref->{'image_type'}\E/i)
) {
return &scan_type_id_to_text($rowref->{'Scan_type'}, $db);
}
} # if ($sd_regex) .... else...
} # foreach my $rowref (@rows)....
} # if(keys %mriProtocolGroupIDs > 1)...else...
} # if (@rows==0)....else...
# if we got here, we're really clueless: insert scan in mri_protocol_violated_scans
# table. Note that $mriProtocolGroupID will be undef unless exactly one protocol
# group was used to try to identify the scan
insert_violated_scans(
$dbhr, $series_description, $minc_location, $patient_name,
$candid, $pscid, $tr, $te,
$ti, $slice_thickness, $xstep, $ystep,
$zstep, $xspace, $yspace, $zspace,
$time, $seriesUID, $tarchiveID, $image_type,
$mriProtocolGroupID
);
return 'unknown';
}
=pod
=head3 insert_violated_scans($dbhr, $series_desc, $minc_location, $patient_name, $candid, $pscid, $visit, $tr, $te, $ti, $slice_thickness, $xstep, $ystep, $zstep, $xspace, $yspace, $zspace, $time, $seriesUID)
Inserts scans that do not correspond to any of the defined protocol from the
C<mri_protocol> table into the C<mri_protocol_violated_scans> table of the
database.
INPUTS:
- $dbhr : database handle reference
- $series_desc : series description of the scan
- $minc_location : location of the MINC file
- $patient_name : patient name of the scan
- $candid : candidate's C<CandID>
- $pscid : candidate's C<PSCID>
- $visit : visit of the scan
- $tr : repetition time of the scan
- $te : echo time of the scan
- $ti : inversion time of the scan
- $slice_thickness: slice thickness of the image
- $xstep : C<x-step> of the image
- $ystep : C<y-step> of the image
- $zstep : C<z-step> of the image
- $xspace : C<x-space> of the image
- $yspace : C<y-space> of the image
- $zspace : C<z-space> of the image
- $time : time dimension of the scan
- $seriesUID : C<SeriesUID> of the scan
- $tarchiveID : C<TarchiveID> of the DICOM archive from which this file is derived
- $image_type : the C<image_type> header value of the image
- $mriProtocolGroupID : ID of the protocol group used to try to identify the scan.
=cut
sub insert_violated_scans {
my ($dbhr, $series_description, $minc_location, $patient_name,
$candid, $pscid, $tr, $te,
$ti, $slice_thickness, $xstep, $ystep,
$zstep, $xspace, $yspace, $zspace,
$time, $seriesUID, $tarchiveID, $image_type,
$mriProtocolGroupID) = @_;
# determine the future relative path when the file will be moved to
# data_dir/trashbin at the end of the script's execution
my $file_rel_path = get_trashbin_file_rel_path($minc_location);
(my $query = <<QUERY) =~ s/\n//gm;
INSERT INTO mri_protocol_violated_scans (
CandID, PSCID, TarchiveID, time_run,
series_description, minc_location, PatientName, TR_range,
TE_range, TI_range, slice_thickness_range, xspace_range,
yspace_range, zspace_range, xstep_range, ystep_range,
zstep_range, time_range, SeriesUID, image_type,
MriProtocolGroupID
) VALUES (
?, ?, ?, now(),
?, ?, ?, ?,
?, ?, ?, ?,
?, ?, ?, ?,
?, ?, ?, ?,
?
)
QUERY
my $sth = $${dbhr}->prepare($query);
my $success = $sth->execute(
$candid, $pscid, $tarchiveID, $series_description,
$file_rel_path, $patient_name, $tr, $te,
$ti, $slice_thickness, $xspace, $yspace,
$zspace, $xstep, $ystep, $zstep,
$time, $seriesUID, $image_type, $mriProtocolGroupID
);
}
=pod
=head3 scan_type_id_to_text($typeID, $db)
Determines the type of the scan identified by its scan type ID.
INPUTS:
- $typeID: scan type ID
- $db : database object
RETURNS: Textual name of scan type
=cut
sub scan_type_id_to_text {
my ($typeID, $db) = @_;
my $mriScanTypeOB = NeuroDB::objectBroker::MriScanTypeOB->new(
db => $db
);
my $mriScanTypeRef = $mriScanTypeOB->get(0, { ID => $typeID });
# This is just to make sure that there is a scan type in the DB
# with name 'unknown' in case we can't find the one with ID $ID
$mriScanTypeOB->get(0, { Scan_type => 'unknown' }) if !@$mriScanTypeRef;
if(!@$mriScanTypeRef) {
NeuroDB::UnexpectedValueException->throw(
errorMessage => sprintf(
"Unknown acquisition protocol ID %d and scan type 'unknown' does not exist in the database",
$typeID
)
);
}
return $mriScanTypeRef->[0]->{'Scan_type'};
}
=pod
=head3 scan_type_text_to_id($type, $db)
Determines the type of the scan identified by scan type.
INPUTS:
- $type: scan type
- $db : database object
RETURNS: ID of the scan type
=cut
sub scan_type_text_to_id {
my($type, $db) = @_;
my $mriScanTypeOB = NeuroDB::objectBroker::MriScanTypeOB->new(
db => $db
);
my $mriScanTypeRef = $mriScanTypeOB->get(
0, { Scan_type => $type }
);
$mriScanTypeRef = $mriScanTypeOB->get(0, { Scan_type => 'unknown' }) if !@$mriScanTypeRef;
if(!@$mriScanTypeRef) {
NeuroDB::UnexpectedValueException->throw(
errorMessage => sprintf(
"Unknown acquisition protocol %s and scan type 'unknown' does not exist in the database",
$type
)
);
}
return $mriScanTypeRef->[0]->{'ID'};
}
=pod
=head3 in_range($value, $range_string)
Determines whether numerical value falls within the range described by range
string. Range string is a single range unit which follows the syntax
"X" or "X-Y".
Note that if C<$range_string>="-", it means that the value in the database are
NULL for both the MIN and MAX columns, therefore we do not want to restrict the
range for this field and the function will return 1.
INPUTS:
- $value : numerical value to evaluate
- $range_string: the range to use
RETURNS: 1 if the value is in range or the range is undef, 0 otherwise
=cut
sub in_range
{
my ($value, $range_string) = @_;
chomp($value);
# return 1 if the range_string = "-" as it means that max & min values were undef
# when calling the in_range function and we should not restrict on that field
return 1 if $range_string eq "-";
# grep the min and max values of the range
my @range = split(/-/, $range_string);
my $min = $range[0];
my $max = $range[1];
# returns 1 if both $min and $max are undefined as in infinity range
return 1 if (!defined $min && !defined $max);
# returns 1 if min & max are defined and value is within the range [min-max]
return 1 if (defined $min && defined $max)
&& ( ($min <= $value && $value <= $max)
|| &floats_are_equal($value, $min, $FLOAT_EQUALS_NB_DECIMALS)
|| &floats_are_equal($value, $max, $FLOAT_EQUALS_NB_DECIMALS)
);
# returns 1 if only min is defined and value is <= to $min
return 1 if (defined $min and !defined $max)
&& ($min <= $value || &floats_are_equal($value, $min, $FLOAT_EQUALS_NB_DECIMALS));
# returns 1 if only max is defined and value is >= to $max
return 1 if (defined $max and !defined $min)
&& ($value <= $max || &floats_are_equal($value, $max, $FLOAT_EQUALS_NB_DECIMALS));
## if we've gotten this far, we're out of range.
return 0;
}
=pod
=head3 floats_are_equal($f1, $f2, $nb_decimals)
Checks whether float 1 and float 2 are equal (considers only the first
C<$nb_decimals> decimals).
INPUTS:
- $f1 : float 1
- $f2 : float 2
- $nb_decimals: the number of first decimals
RETURNS: 1 if the numbers are relatively equal, 0 otherwise
=cut
sub floats_are_equal {
my($f1, $f2, $nb_decimals) = @_;
return sprintf("%.${nb_decimals}g", $f1) eq sprintf("%.${nb_decimals}g", $f2);
}
=pod
=head3 register_db($file_ref)
Registers the C<NeuroDB::File> object referenced by C<$file_ref> into the
database.
INPUT: file hash ref
RETURNS: 0 if the file is already registered, the new C<FileID> otherwise
=cut
sub register_db {
my ($file_ref) = @_;
my $file = $$file_ref;
# get the database handle
my $dbh = ${$file->getDatabaseHandleRef()};
# retrieve the file's data
my $fileData = $file->getFileData();
# make sure this file isn't registered
if(defined($fileData->{'FileID'}) && $fileData->{'FileID'} > 0) {
return 0;
}
# build the insert query
my $query = "INSERT INTO files SET ";
foreach my $key ('File', 'SessionID','EchoTime', 'CoordinateSpace', 'OutputType', 'AcquisitionProtocolID', 'FileType', 'InsertedByUserID', 'Caveat', 'SeriesUID', 'TarchiveSource','SourcePipeline','PipelineDate','SourceFileID', 'ScannerID') {
# add the key=value pair to the query
$query .= "$key=".$dbh->quote($${fileData{$key}}).", ";
}
$query .= "InsertTime=UNIX_TIMESTAMP()";
# run the query
$dbh->do($query);
my $fileID = $dbh->{'mysql_insertid'};
$file->setFileData('FileID', $fileID);
# retrieve the file's parameters
my $params = $file->getParameters();
# if there are any parameters to save
if(scalar(keys(%$params)) > 0) {
# build the insert query
$query = "INSERT INTO parameter_file (FileID, ParameterTypeID, Value, InsertTime) VALUES ";
foreach my $key (keys %$params) {
# skip the parameter if it is not defined
next unless defined $${params{$key}};
# add the parameter to the query
my $typeID = $file->getParameterTypeID($key);
my $value = '';
$value = $dbh->quote($${params{$key}});
if($query =~ /\)$/) { $query .= ",\n"; }
$query .= "($fileID, $typeID, $value, UNIX_TIMESTAMP())";
}
# run query
$dbh->do($query);
}
return $fileID;
}
=pod
=head3 mapDicomParameters($file_ref)
Maps DICOM parameters to more meaningful names in the C<NeuroDB::File> object
referenced by C<$file_ref>.
INPUT: file hash ref
=cut
sub mapDicomParameters {
my ($file_ref) = @_;
my $file = $$file_ref;
my (%map_hash);
%map_hash=
(
xstep => 'xspace:step',
ystep => 'yspace:step',
zstep => 'zspace:step',
xstart => 'xspace:start',
ystart => 'yspace:start',
zstart => 'zspace:start',
study_date => 'dicom_0x0008:el_0x0020',
series_date => 'dicom_0x0008:el_0x0021',
acquisition_date => 'dicom_0x0008:el_0x0022',
image_date => 'dicom_0x0008:el_0x0023',
study_time => 'dicom_0x0008:el_0x0030',
series_time => 'dicom_0x0008:el_0x0031',
acquisition_time => 'dicom_0x0008:el_0x0032',
image_time => 'dicom_0x0008:el_0x0033',
modality => 'dicom_0x0008:el_0x0060',
manufacturer => 'dicom_0x0008:el_0x0070',
institution_name =>'dicom_0x0008:el_0x0080',
study_description => 'dicom_0x0008:el_0x1030',
series_description => 'dicom_0x0008:el_0x103e',
operator_name => 'dicom_0x0008:el_0x1070',
manufacturer_model_name => 'dicom_0x0008:el_0x1090',
patient_name => 'dicom_0x0010:el_0x0010',
patient_id => 'dicom_0x0010:el_0x0020',
patient_dob => 'dicom_0x0010:el_0x0030',
patient_sex => 'dicom_0x0010:el_0x0040',
scanning_sequence => 'dicom_0x0018:el_0x0020',
mr_acquisition_type => 'dicom_0x0018:el_0x0023',
sequence_name => 'dicom_0x0018:el_0x0024',
sequence_variant => 'dicom_0x0018:el_0x0021',
slice_thickness => 'dicom_0x0018:el_0x0050',
effective_series_duration => 'dicom_0x0018:el_0x0072',
repetition_time => 'acquisition:repetition_time',
echo_time => 'acquisition:echo_time',
inversion_time => 'acquisition:inversion_time',
number_of_averages => 'dicom_0x0018:el_0x0083',
imaging_frequency => 'dicom_0x0018:el_0x0084',
imaged_nucleus => 'dicom_0x0018:el_0x0085',
echo_numbers => 'dicom_0x0018:el_0x0086',
magnetic_field_strength => 'dicom_0x0018:el_0x0087',
spacing_between_slices => 'dicom_0x0018:el_0x0088',
number_of_phase_encoding_steps => 'dicom_0x0018:el_0x0089',
echo_train_length => 'dicom_0x0018:el_0x0091',
percent_sampling => 'dicom_0x0018:el_0x0093',
percent_phase_field_of_view => 'dicom_0x0018:el_0x0094',
pixel_bandwidth => 'dicom_0x0018:el_0x0095',
device_serial_number => 'dicom_0x0018:el_0x1000',
software_versions => 'dicom_0x0018:el_0x1020',
protocol_name => 'dicom_0x0018:el_0x1030',
spatial_resolution => 'dicom_0x0018:el_0x1050',
fov_dimensions => 'dicom_0x0018:el_0x1149',
receiving_coil => 'dicom_0x0018:el_0x1250',
transmitting_coil => 'dicom_0x0018:el_0x1251',
acquisition_matrix => 'dicom_0x0018:el_0x1310',
phase_encoding_direction => 'dicom_0x0018:el_0x1312',
variable_flip_angle_flag => 'dicom_0x0018:el_0x1315',
sar => 'dicom_0x0018:el_0x1316',
patient_position => 'dicom_0x0018:el_0x5100',
study_instance_uid => 'dicom_0x0020:el_0x000d',
series_instance_uid => 'dicom_0x0020:el_0x000e',
study_id => 'dicom_0x0020:el_0x0010',
series_number => 'dicom_0x0020:el_0x0011',
acquisition_number => 'dicom_0x0020:el_0x0012',
instance_number => 'dicom_0x0020:el_0x0013',
image_position_patient => 'dicom_0x0020:el_0x0032',
image_orientation_patient => 'dicom_0x0020:el_0x0037',
frame_of_reference_uid => 'dicom_0x0020:el_0x0052',
laterality => 'dicom_0x0020:el_0x0060',
position_reference_indicator => 'dicom_0x0020:el_0x1040',
slice_location => 'dicom_0x0020:el_0x1041',
image_comments => 'dicom_0x0020:el_0x4000',
rows => 'dicom_0x0028:el_0x0010',
cols => 'dicom_0x0028:el_0x0011',
pixel_spacing => 'dicom_0x0028:el_0x0030',
bits_allocated => 'dicom_0x0028:el_0x0100',
bits_stored => 'dicom_0x0028:el_0x0101',
high_bit => 'dicom_0x0028:el_0x0102',
pixel_representation => 'dicom_0x0028:el_0x0103',
smallest_pixel_image_value => 'dicom_0x0028:el_0x0106',
largest_pixel_image_value => 'dicom_0x0028:el_0x0107',
pixel_padding_value => 'dicom_0x0028:el_0x0120',
window_center => 'dicom_0x0028:el_0x1050',
window_width => 'dicom_0x0028:el_0x1051',
window_center_width_explanation => 'dicom_0x0028:el_0x1055'
);
# map parameters, removing the old params if they start with 'dicom'
foreach my $key (keys %map_hash) {
my $value = $file->getParameter($map_hash{$key});
if(defined $value) {
$file->setParameter($key, $value);
$file->removeParameter($map_hash{$key}) if($map_hash{$key} =~ /^dicom/);
}
}
my $patientName = $file->getParameter('patient_name');
$patientName =~ s/[\?\(\)\\\/\^]//g;
$file->setParameter('patient_name', $patientName);
$patientName = $file->getParameter('patient:full_name');
$patientName =~ s/[\?\(\)\\\/\^]//g;
$file->setParameter('patient:full_name', $patientName);
}
=pod
=head3 findScannerID($manufacturer, $model, $serialNumber, $softwareVersion, $centerID, $dbhr, $db)
Finds the scanner ID for the scanner as defined by C<$manufacturer>, C<$model>,
C<$serialNumber>, C<$softwareVersion>, using the database attached to the DBI
database handle reference C<$dbhr>. If no scanner ID exists, one will be
created.
INPUTS:
- $manufacturer : scanner's manufacturer
- $model : scanner's model
- $serialNumber : scanner's serial number
- $softwareVersion: scanner's software version
- $centerID : scanner's center ID
- $dbhr : database handle reference
- $db : database object
RETURNS: (int) scanner ID
=cut
sub findScannerID {
my ($manufacturer, $model, $serialNumber, $softwareVersion, $centerID, $dbhr, $db) = @_;
my $mriScannerOB = NeuroDB::objectBroker::MriScannerOB->new( db => $db );
my $resultsRef = $mriScannerOB->get( {
Manufacturer => $manufacturer,
Model => $model,
Software => $softwareVersion,
Serial_number => $serialNumber
});
# Scanner exists
return $resultsRef->[0]->{'ID'} if @$resultsRef;
# register new scanners
my $scanner_id = registerScanner($manufacturer, $model, $serialNumber, $softwareVersion, $centerID, $dbhr, $db);
return $scanner_id;
}
=pod
=head3 registerScanner($manufacturer, $model, $serialNumber, $softwareVersion, $centerID, $dbhr, $db)
Registers the scanner as defined by C<$manufacturer>, C<$model>,
C<$serialNumber>, C<$softwareVersion>, into the database attached to the DBI
database handle reference C<$dbhr>.
INPUTS:
- $manufacturer : scanner's manufacturer
- $model : scanner's model
- $serialNumber : scanner's serial number
- $softwareVersion: scanner's software version
- $centerID : scanner's center ID
- $dbhr : database handle reference
- $db : database object
RETURNS: (int) scanner ID
=cut
sub registerScanner {
my ($manufacturer, $model, $serialNumber, $softwareVersion, $centerID, $dbhr, $db) = @_;