PetHRRT pipeline fixes

README.md

@@ -10,6 +10,7 @@ This repo can be installed on the same VM as the main LORIS codebase, or on a di
  * Python 3 with pip3 and virtualenv (step 2 below)
  * MINC toolkit (step 3 below)
  * DICOM toolkit (step 4 below)
+ * tpcclib (for hrrt only) (http://www.turkupetcentre.net/tpcclib-doc/md_install.html)
 
 On <u>Ubuntu</u>, DICOM toolkit will be installed by the imaging install script (step 4 below). This script will _apt-get install dcmtk_.   
 

batch_uploads_imageuploader.pl

@@ -161,15 +161,13 @@ =head2 Methods
 my ($stdoutbase, $stderrbase) = ("$data_dir/batch_output/imuploadstdout.log", 
 				 "$data_dir/batch_output/imuploadstderr.log");
 
-
-while($_ = $ARGV[0], /^-/) {
+while($_ = $ARGV[0] // '', /^-/) {
     shift;
     last if /^--$/; ## -- ends argument processing
     if (/^-D/) { $debug++ } ## debug level
     if (/^-v/) { $verbose++ } ## verbosity
 }
 
-
 ## read input from STDIN, store into array @inputs (`find ....... | this_script`)
 my @patientnamearray = ();
 my @fullpatharray = ();

imaging_install.sh

@@ -114,6 +114,7 @@ echo "Creating the data directories"
   sudo -S su $USER -c "mkdir -m 2770 -p /data/$PROJ/data/"
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/trashbin"         #holds mincs that didn't match protocol
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/tarchive"         #holds tared dicom-folder
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/hrrtarchive"      #holds tared hrrt-folder
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/pic"              #holds jpegs generated for the MRI-browser
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/logs"             #holds logs from pipeline script
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/assembly"         #holds the MINC files

imaging_install_MacOSX.sh

@@ -45,6 +45,7 @@ echo "Creating the data directories"
   sudo -S su $USER -c "chmod g+s /data/$PROJ/data/"
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/trashbin"          #holds mincs that didn't match protocol
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/tarchive"          #holds tared dicom-folder
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/hrrtarchive"       #holds tared hrrt-folder
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/pic"               #holds jpegs generated for the MRI-browser
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/logs"              #holds logs from pipeline script
   sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/assembly"          #holds the MINC files

uploadNeuroDB/HRRT_PET_insertion.pl

@@ -607,4 +607,4 @@ sub run_hrrt_archival {
     $archive->{hrrt_archive_ID} = $newHrrtArchiveID;
 
     return $archive;
-}
+}

uploadNeuroDB/NeuroDB/ExitCodes.pm

@@ -201,13 +201,14 @@ our $REGISTER_PROGRAM_FAILURE = 200; # if MNI::Spawn::RegisterPrograms failed
 
 
 #### --- FROM uploadNeuroDB/HRRT_PET_insertion.pl
-our $INVALID_UPLOAD_ID       = 280; # invalid upload ID
-our $INVALID_UPLOAD_LOCATION = 281; # invalid upload location
-our $INVALID_DECOMP_LOCATION = 282; # invalid decompressed location
-our $MINC_FILE_NOT_FOUND     = 283; # if could not convert ECAT file into MINC
-our $MINC_INSERTION_FAILURE  = 284; # if MINC file insertion failure
-our $HRRT_ALREADY_INSERTED   = 285; # if HRRT archive already exists in DB
-our $HEADER_INSERT_FAILURE   = 286; # if could not insert matlab info into the
-                                    # MINC header
+our $INVALID_UPLOAD_ID              = 280; # invalid upload ID
+our $INVALID_UPLOAD_LOCATION        = 281; # invalid upload location
+our $INVALID_DECOMP_LOCATION        = 282; # invalid decompressed location
+our $MINC_FILE_NOT_FOUND            = 283; # if could not convert ECAT file into MINC
+our $MINC_INSERTION_FAILURE         = 284; # if MINC file insertion failure
+our $HRRT_ALREADY_INSERTED          = 285; # if HRRT archive already exists in DB
+our $HEADER_INSERT_FAILURE          = 286; # if could not insert matlab info into the
+                                           # MINC header
 our $HRRT_ARCHIVE_INSERTION_FAILURE = 287; # if HRRT archive insertion into the
                                            # database has failed
+our $UNKNOW_PROTOCOL                = 288; # if HRRT protocol is not found

uploadNeuroDB/NeuroDB/HRRT.pm

@@ -47,7 +47,6 @@ use Date::Parse;
 use String::ShellQuote;
 use File::Copy;
 
-
 use NeuroDB::MincUtilities;
 use NeuroDB::Utilities;
 
@@ -303,16 +302,18 @@ sub read_matlab_file {
     my @matlab_files = grep ( /.m$/, @{ $self->{hrrt_files} } );
     my $matlab_file  = $matlab_files[0];
 
-    open my $fh, '<', $matlab_file;
-    chomp(my @info = <$fh>);
-    close $fh;
-
-    foreach my $line_nb ( @info ) {
-        next unless ( $line_nb =~ / = / );
-        my ($key, $val) = split( ' = ', $line_nb );
-        $val =~ s/;\cM$//;
-        # set header information
-        $self->{matlab_info}->{$key} = $val;
+    if (defined($matlab_file)) {
+        open my $fh, '<', $matlab_file;
+        chomp(my @info = <$fh>);
+        close $fh;
+
+        foreach my $line_nb ( @info ) {
+            next unless ( $line_nb =~ / = / );
+            my ($key, $val) = split( ' = ', $line_nb );
+            $val =~ s/;\cM$//;
+            # set header information
+            $self->{matlab_info}->{$key} = $val;
+        }
     }
 
     return $self->{matlab_info};
@@ -753,4 +754,4 @@ License: GPLv3
 
 LORIS community <loris.info@mcin.ca> and McGill Centre for Integrative Neuroscience
 
-=cut
+=cut

uploadNeuroDB/NeuroDB/ImagingUpload.pm

@@ -282,8 +282,8 @@ sub IsCandidateInfoValid {
         }
     }
 
-	# Issue a warning for the total number of files that are not
-	# DICOM images
+    # Issue a warning for the total number of files that are not
+    # DICOM images
     my $files_not_dicom = scalar @non_image_files;
     if ( (!$this->{'is_hrrt'}) && ($files_not_dicom > 0) ) {
         $message = "\nWARNING: There are $files_not_dicom file(s) which"
@@ -295,6 +295,7 @@ sub IsCandidateInfoValid {
     my $phantom_regex = "($lego_phantom_regex)|($living_phantom_regex)";
     my $patient_name  = $this->{'pname'};
     if ($this->{'is_hrrt'}) {
+
         # if modality is PET HRRT (i.e. there's at least one ECAT7 file), then check
         # that all the files present in the PET directory have been named correctly
         foreach my $file (@file_list) {
@@ -312,7 +313,7 @@ sub IsCandidateInfoValid {
         }
     }
 
-    # return 0 if found at least one DICOM file without the proper patient name
+    # return > 0 if found at least one DICOM file without the proper patient name
     if ( $files_with_unmatched_patient_name > 0 ) {
         $message =
             "\nERROR: There are $files_with_unmatched_patient_name file(s)"

uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm

@@ -171,12 +171,15 @@ INPUTS:
 
 sub writeErrorLog {
     my $this = shift;
-    my ($message, $failStatus,$LogDir) = @_;
+    my ($message, $failStatus, $LogDir) = @_;
     print STDERR $message;
     $this->{LOG}->print($message);
-    $this->{LOG}->print(
-        "program exit status: $failStatus"
-    );
+
+    if (defined($failStatus)) {
+        $this->{LOG}->print(
+            "program exit status: $failStatus"
+        );
+    }
     `cat $this->{logfile}  >> $this->{LogDir}/error.log`;
     close $this->{LOG};
     `rm -f $this->{logfile} `;
@@ -463,7 +466,7 @@ sub createTarchiveArray {
     if ($hrrt) {
 
         my %tarchiveInfo;
-        my ($query = <<QUERY) =~ s/\n/ /gm;
+        (my $query = <<QUERY) =~ s/\n/ /gm;
         SELECT
           PatientName,    CenterName,      DateAcquired,
           Blake2bArchive, ArchiveLocation, HrrtArchiveID
@@ -472,9 +475,11 @@ sub createTarchiveArray {
         WHERE
           ArchiveLocation LIKE ?
 QUERY
+
         if ($this->{debug}) {
             print $query . "\n";
         }
+
         my $sth = ${$this->{'dbhr'}}->prepare($query);
         $sth->execute("'%".basename($tarchive)."%'");
 

uploadNeuroDB/NeuroDB/Utilities.pm

@@ -48,4 +48,7 @@ sub blake2b_hash {
     binmode(FILE);
 
     return Digest::BLAKE2->new->addfile(*FILE)->hexdigest;
-}
+}
+
+1;
+