Adopt new DICOM study importer in the MRI pipeline

dicom-archive/dicomTar.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 # J-Sebastian Muehlboeck 2006
 # sebas@bic.mni.mcgill.ca
-# Archive your dicom data using DICOM::DCMSUM 
+# Archive your dicom data using DICOM::DCMSUM
 # Tar and gzip dicom files and retar them with pertaining summary and creation log
 # @VERSION : $Id: dicomTar.pl 9 2007-12-18 22:26:00Z jharlap $
 
@@ -133,6 +133,10 @@ =head2 Methods
      exit."],
      );
 
+print STDERR "WARNING: `dicomTar.pl` is deprecated and may eventually be removed. Please use the"
+             . " new `import_dicom_study.py` script instead, which also comes with new features"
+             . " like support for enhanced DICOMs, multi-echo series, and more.\n\n";
+
 GetOptions(\@arg_table, \@ARGV) ||  exit $NeuroDB::ExitCodes::GETOPT_FAILURE;
 
 if ($version) { print "Version: $versionInfo\n"; exit; }
@@ -171,7 +175,7 @@ =head2 Methods
     exit $NeuroDB::ExitCodes::MISSING_ARG;
 }
 
-# The tar target 
+# The tar target
 my $totar = basename($dcm_source);
 print "Source: ". $dcm_source . "\nTarget: ".  $targetlocation . "\n\n"
     if $verbose;
@@ -187,7 +191,7 @@ =head2 Methods
     print "Database is available.\n\n" if $verbose;
 }
 
-# ***************************************    main    *************************************** 
+# ***************************************    main    ***************************************
 #### get some info about who created the archive and where and when
 my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst)=localtime(time);
 my $date            = sprintf("%4d-%02d-%02d %02d:%02d:%02d\n",
@@ -217,7 +221,7 @@ =head2 Methods
 # get the unique study ID
 my $studyUnique = $summary->{'studyuid'};
 my $creator         = $summary->{user};
-my $sumTypeVersion  = $summary->{sumTypeVersion}; 
+my $sumTypeVersion  = $summary->{sumTypeVersion};
 
 # check if the study is already uploaded in the tarchive tables
 if ($dbase) {
@@ -246,7 +250,7 @@ =head2 Methods
     exit $NeuroDB::ExitCodes::TARGET_EXISTS_NO_CLOBBER;
 }
 
-# read acquisition metadata into variable 
+# read acquisition metadata into variable
 my $metafile = "$targetlocation/$metaname.meta";
 open META, ">$metafile";
 META->autoflush(1);
@@ -260,7 +264,7 @@ =head2 Methods
 # get rid of newline
 chomp($hostname,$system);
 
-#### create tar from rigt above the source 
+#### create tar from rigt above the source
 chdir(dirname($dcm_source));
 print "You will archive the dir\t\t: $totar\n" if $verbose;
 # tar contents into tarball
@@ -283,7 +287,7 @@ =head2 Methods
 &archive_head;
 close TARINFO;
 select(STDOUT);
-my $tarinfo = &read_file("$totar.log"); 
+my $tarinfo = &read_file("$totar.log");
 
 my $retar = "tar cvf DCM\_$byDate\_$totar.tar $totar.meta $totar.log $totar.tar.gz";
 `$retar`;
@@ -295,7 +299,7 @@ =head2 Methods
 &archive_head;
 close TARINFO;
 select(STDOUT);
-$tarinfo = &read_file("$totar.log"); 
+$tarinfo = &read_file("$totar.log");
 print  $tarinfo if $verbose;
 
 
@@ -343,7 +347,7 @@ =head2 Methods
 
 exit $NeuroDB::ExitCodes::SUCCESS;
 
-=pod 
+=pod
 
 =head3 archive_head()
 
@@ -363,11 +367,11 @@ sub archive_head {
 * Archive target location          :    @<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
                                       $finalTarget,
 * Name of creating host            :    @<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-                                      $hostname,                                
+                                      $hostname,
 * Name of host OS                  :    @<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
                                       $system,
 * Created by user                  :    @<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-                                      $creator,                                
+                                      $creator,
 * Archived on                      :    @<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
                                       $date,
 * dicomSummary version             :    @<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -382,7 +386,7 @@ sub archive_head {
                                       $ARCHIVEmd5sum,
 .
 
-=pod 
+=pod
 
 =head3 read_file($file)
 

docs/scripts_md/ConfigOB.md

@@ -61,7 +61,7 @@ RETURN: new instance of this class.
 
 ### &$getConfigSettingRef($setting)
 
-Private method. This method fetches setting `$setting` from the LORIS table 
+Private method. This method fetches setting `$setting` from the LORIS table
 Config. It will throw a `NeuroDB::objectBroker::ObjectBrokerException` if either
 the database transaction failed for some reason or it succeeded but returned no
 results (i.e. setting `$setting` does not exist).
@@ -262,6 +262,13 @@ Get the bids\_validator\_options\_to\_ignore Config setting
 RETURN: an array of the BIDS validator options to ignore
 to use when creating a BIDS dataset
 
+### getUseLegacyDicomStudyImporter()
+
+Get the use\_legacy\_dicom\_study\_importer Config setting
+
+RETURN: (boolean) 1 if use\_legacy\_dicom\_study\_importer is set to Yes in the Config module, 0
+otherwise
+
 # TO DO
 
 Nothing planned.

docs/scripts_md/GetRole.md

@@ -108,7 +108,6 @@ INPUTS:
        Field3 => undef
      }
 
-
 RETURNS:
    - a reference to an array of hash references. Every hash contains the values
      for a given row returned by the method call: the key/value pairs contain
@@ -135,6 +134,5 @@ INPUTS:
        Field3 => undef
      }
 
-
 RETURNS:
    - the number of records found.

docs/scripts_md/MRI.md

@@ -56,10 +56,10 @@ 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 
+  - $dbh         : database handle
   - $db          : database object
 
-RETURNS: an array of 2 elements: 
+RETURNS: an array of 2 elements:
   - A reference to a hash containing the session properties:
     `ID` => session ID.
     `ProjectID` => project ID for the session.
@@ -429,7 +429,6 @@ that could not be deleted.
 INPUTS:
 
     - @files: list of files to delete.
-
 
 # TO DO
 

docs/scripts_md/MRIProcessingUtility.md

@@ -45,7 +45,7 @@ Creates a new instance of this class. The parameter `$dbhr` is a reference
 to a `DBI` database handle, used to set the object's database handle, so that
 all the DB-driven methods will work.
 
-INPUT: 
+INPUT:
   - $db      : database object
   - $dbhr    : DBI database handle reference
   - $debug   : degug flag (1 for debug, 0 otherwise)
@@ -117,9 +117,9 @@ RETURNS:
 
 This function does:
 1) Determine subject's ID based on scanner ID and DICOM archive information.
-2) Call the `CreateMRICandidate` function (will create the candidate if it does 
+2) Call the `CreateMRICandidate` function (will create the candidate if it does
 not exists and `createCandidates` config option is set to yes)
-3) Call the `validateCandidate` to validate the candidate information 
+3) Call the `validateCandidate` to validate the candidate information
 (it will return a `CandMismatchError` if there is one)
 
 INPUTS:
@@ -181,7 +181,7 @@ RETURNS: project ID
 
 ### determineScannerID($tarchiveInfo, $to\_log, $centerID, $projectID, $upload\_id)
 
-Determines which scanner ID was used for DICOM acquisitions. Note, if 
+Determines which scanner ID was used for DICOM acquisitions. Note, if
 a scanner ID is not already associated to the scanner information found
 in the DICOM headers, then a new scanner will automatically be created.
 
@@ -391,7 +391,7 @@ Registers a new candidate in the `candidate` table.
 
 Note: before doing so, the following checks will be performed:
 1) check that the `createCandidates` config option was set to yes
-2) check that the `PSCID` given in `$subjectIDsref` is not already associated 
+2) check that the `PSCID` given in `$subjectIDsref` is not already associated
 to an existing candidate
 3) check that the `CandID` given in `$subjectIDsref` is not already associated
 to an existing candidate
@@ -438,8 +438,8 @@ RETURNS: the final directory in which the registered MINC files will go
 
 Check that the candidate's information derived from the patient name field of
 the DICOM files is valid (`CandID` and `PSCID` of the candidate should
-correspond to the same subject in the database). It will also check that the 
-Visit Label of `$subjectIDsref` is a valid Visit Label present in the 
+correspond to the same subject in the database). It will also check that the
+Visit Label of `$subjectIDsref` is a valid Visit Label present in the
 `Visit_Windows` table.
 
 INPUT: subject's ID information hash ref

docs/scripts_md/batch_uploads_tarchive.md

@@ -10,11 +10,11 @@ batch\_uploads\_tarchive - upload a batch of DICOM archives using script
 # DESCRIPTION
 
 This script uploads a list of DICOM archives to the database by calling script
-`tarchiveLoader.pl` on each file in succession. The list of files to process is read 
+`tarchiveLoader.pl` on each file in succession. The list of files to process is read
 from `STDIN`, one file name per line. Each file name is assumed to be a path
 relative to `tarchiveLibraryDir` (see below).
 
-The following settings of file `$ENV{LORIS_CONFIG}/.loris-mri/prod` affect the 
+The following settings of file `$ENV{LORIS_CONFIG}/.loris-mri/prod` affect the
 behvaviour of `batch_uploads_tarchive` (where `$ENV{LORIS_CONFIG}` is the
 value of the Unix environment variable `LORIS_CONFIG`):