Added a tool to sort unsorted dicomfiles to the 3-digit SeriesNumber-SeriesDescription format as in /raw

Author: marcelzwiers

bidscoiner/dicomsort.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+"""
+Sorts DICOM files into local subdirectories with a (3-digit) SeriesNumber-SeriesDescription directory name (i.e. following the same listing as on the scanner console)
+"""
+
+import os
+import re
+import bids
+import warnings
+
+
+def sortsession(sessionfolder, pattern):
+    """
+    Sorts dicomfiles into (3-digit) SeriesNumber-SeriesDescription subfolders (e.g. '003-T1MPRAGE')
+
+    :param str sessionfolder:   The name of the folder that contains the dicom files
+    :param str pattern:         The regular expression pattern used in re.match() to select the dicom files
+    :return:                    Nothing
+    :rtype: NoneType
+    """
+
+    # Input checking
+    sessionfolder = os.path.abspath(os.path.expanduser(sessionfolder))
+    seriesdirs    = []
+    print('> Sorting: ' + sessionfolder)
+
+    # Map all dicomfiles and move them to series folders
+    for dicomfile in [os.path.join(sessionfolder,dcmfile) for dcmfile in os.listdir(sessionfolder) if re.match(pattern, dcmfile)]:
+
+        # Extract the SeriesDescription and SeriesNumber from the dicomfield
+        seriesnr    = bids.get_dicomfield('SeriesNumber', dicomfile)
+        seriesdescr = bids.get_dicomfield('SeriesDescription', dicomfile)
+        if not seriesdescr:
+            seriesdescr = bids.get_dicomfield('ProtocolName', dicomfile)
+            if not seriesdescr:
+                seriesdescr = 'unknown_protocol'
+                warnings.warn('No SeriesDecription or ProtocolName found for: ' + dicomfile)
+
+        # Create the series subfolder
+        seriesdir = '{:03d}-{}'.format(seriesnr, seriesdescr)
+        if seriesdir not in seriesdirs:                 # We have a new series
+            if not os.path.isdir(os.path.join(sessionfolder, seriesdir)):
+                print('Creating:  ' + os.path.join(sessionfolder, seriesdir))
+                os.makedirs(os.path.join(sessionfolder, seriesdir))
+            seriesdirs.append(seriesdir)
+
+        # Move the dicomfile to the series subfolder
+        os.rename(dicomfile, os.path.join(sessionfolder, seriesdir, os.path.basename(dicomfile)))
+
+
+def sortsessions(rawfolder, subjectid='', sessionid='', pattern='.*\.(IMA|dcm)$'):
+    """
+
+    :param rawfolder:   The root folder containing the source [sub/][ses/]dicomfiles
+    :param subjectid:   The prefix of the sub folders in rawfolder
+    :param sessionid:   The prefix of the ses folders in sub folder
+    :param pattern:     The regular expression pattern used in re.match() to select the dicom files
+    :return:            Nothing
+    :rtype: NoneType
+    """
+
+    if subjectid:
+        for subfolder in bids.lsdirs(os.path.join(rawfolder, subjectid + '*')):
+            if sessionid:
+                for sesfolder in bids.lsdirs(os.path.join(subfolder, sessionid + '*')):
+                    sortsession(sesfolder, pattern)
+            else:
+                sortsession(subfolder, pattern)
+    else:
+        sortsession(rawfolder, pattern)
+
+
+# Shell usage
+if __name__ == "__main__":
+
+    # Parse the input arguments and run the sortsessions(args)
+    import argparse
+    import textwrap
+    parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,
+                                     description=textwrap.dedent(__doc__),
+                                     epilog='examples:\n  rawmapper.py -r /project/3022026.01/raw\n  rawmapper.py -d AcquisitionDate /project/3022026.01/raw\n ')
+    parser.add_argument('rawfolder',   help='The root folder containing the source [sub/][ses/]dicomfiles')
+    parser.add_argument('--subjectid', help='The prefix of the subject folders in rawfolder (empty value means no recursive search)', default='')
+    parser.add_argument('--sessionid', help='The prefix of the session folders in the subject folder (empty value means no recursive search)', default='')
+    parser.add_argument('--pattern',   help='The regular expression pattern used in re.match() to select the dicom files', default='.*\.(IMA|dcm)$')
+    args = parser.parse_args()
+
+    sortsessions(rawfolder=args.rawfolder, subjectid=args.subjectid, sessionid=args.sessionid, pattern=args.pattern)