Ability to specify external command to generate acquisition uid

.travis.yml

@@ -6,8 +6,8 @@ python:
 env:
     global:
         - DCMTK_VERSION="dcmtk-3.6.1_20150924"
-        - DCMTK_DB_DIR="dcmtk_dicom_db"
-        - TESTDATA_DIR="testdata"
+        - DCMTK_DB_DIR="dcmtk_dicom_db-ci"
+        - TESTDATA_DIR="testdata-ci"
         - ORTHANC_VERSION="Orthanc-1.1.0"
 
 cache:
@@ -33,7 +33,7 @@ install:
 
 script:
     - ./test/test.sh
-    - ./test/lint.sh reaper
+    - ./test/lint.sh
 
 after_success:
     - ./docker/build-trigger.sh Tag "${TRAVIS_TAG}" "${BUILD_TRIGGER_URL}"

reaper/dcm.py

@@ -1,10 +1,11 @@
 """SciTran Reaper DICOM utility functions"""
 
-import os
-import shutil
+import datetime
 import hashlib
 import logging
-import datetime
+import os
+import shlex
+import subprocess
 
 import dicom
 
@@ -17,7 +18,25 @@
 GEMS_TYPE_VXTL = ['DERIVED', 'SECONDARY', 'VXTL STATE']
 
 
-def pkg_series(_id, path, map_key, opt_key=None, anonymize=False, timezone=None):
+class DicomError(Exception):
+
+    """DicomError class"""
+
+    pass
+
+
+def __external_metadata(command, filepath):
+    try:
+        args = shlex.split(command) + [filepath]
+        log.debug('External metadata cmd: %s', ' '.join(args))
+        return subprocess.check_output(args)
+    except subprocess.CalledProcessError as ex:
+        msg = 'Error running external command. Exit code %d' % ex.returncode
+        log.error(msg)
+        raise DicomError(msg)
+
+
+def pkg_series(_id, path, map_key, opt_key=None, anonymize=False, timezone=None, additional_metadata=None):
     # pylint: disable=missing-docstring
     dcm_dict = {}
     log.info('inspecting   %s', _id)
@@ -38,27 +57,37 @@ def pkg_series(_id, path, map_key, opt_key=None, anonymize=False, timezone=None)
                 filename = filename.replace('(none)', 'NA')
             file_time = max(int(dcm.acquisition_timestamp.strftime('%s')), 315561600)  # zip can't handle < 1980
             os.utime(filepath, (file_time, file_time))  # correct timestamps
-            os.rename(filepath, '%s.dcm' % os.path.join(arcdir_path, filename))
+            arc_filepath = '%s.dcm' % os.path.join(arcdir_path, filename)
+            os.rename(filepath, arc_filepath)
         arc_path = util.create_archive(arcdir_path, dir_name)
-        metadata = util.object_metadata(dcm, timezone, os.path.basename(arc_path))
+        for md_group_info in (additional_metadata or {}).itervalues():
+            for md_field, md_value in md_group_info.iteritems():
+                if md_value.startswith('^'):    # DICOM header value
+                    md_group_info[md_field] = dcm.raw_header.get(md_value[1:], None)
+                elif md_value.startswith('@'):  # external command
+                    md_group_info[md_field] = __external_metadata(md_value[1:], arc_filepath)
+                else:                           # verbatim value
+                    md_group_info[md_field] = md_value[1:]
+        metadata = util.object_metadata(dcm, timezone, os.path.basename(arc_path), additional_metadata)
         util.set_archive_metadata(arc_path, metadata)
-        shutil.rmtree(arcdir_path)
         metadata_map[arc_path] = metadata
     return metadata_map
 
 
 class DicomFile(object):
 
-    """
-    DicomFile class
-    """
+    """DicomFile class"""
 
     # pylint: disable=too-few-public-methods
 
     def __init__(self, filepath, map_key, opt_key=None, parse=False, anonymize=False, timezone=None):
         if not parse and anonymize:
-            raise Exception('Cannot anonymize DICOM file without parsing')
-        dcm = dicom.read_file(filepath, stop_before_pixels=(not anonymize))
+            raise DicomError('Cannot anonymize DICOM file without parsing')
+        try:
+            dcm = dicom.read_file(filepath, stop_before_pixels=(not anonymize))
+        except:
+            raise DicomError()
+        self.raw_header = dcm
         self._id = dcm.get(map_key, '')
         self.opt = dcm.get(opt_key, '') if opt_key else None
         self.acq_no = str(dcm.get('AcquisitionNumber', '')) or None if dcm.get('Manufacturer').upper() != 'SIEMENS' else None

reaper/dicom_reaper.py

@@ -19,6 +19,8 @@ def __init__(self, options):
         self.scu = scu.SCU(options.get('host'), options.get('port'), options.get('return_port'), options.get('aet'), options.get('aec'))
         super(DicomReaper, self).__init__(self.scu.aec, options)
         self.anonymize = options.get('anonymize')
+        self.additional_metadata = {group: {field: value} for group, field, value in options.get('metadata')}
+        print self.additional_metadata
 
         self.query_tags = {self.map_key: ''}
         if self.opt_key is not None:
@@ -55,6 +57,7 @@ def instrument_query(self):
         return i_state
 
     def reap(self, _id, item, tempdir):
+        # pylint: disable=too-many-return-statements
         if item['state']['images'] == 0:
             log.info('ignoring     %s (zero images)', _id)
             return None, {}
@@ -68,13 +71,20 @@ def reap(self, _id, item, tempdir):
         success, reap_cnt = self.scu.move(scu.SeriesQuery(SeriesInstanceUID=_id), reapdir)
         log.info('reaped       %s (%d images) in %.1fs', _id, reap_cnt, (datetime.datetime.utcnow() - reap_start).total_seconds())
         if success and reap_cnt > 0:
-            df = dcm.DicomFile(os.path.join(reapdir, os.listdir(reapdir)[0]), self.map_key, self.opt_key)
+            try:
+                df = dcm.DicomFile(os.path.join(reapdir, os.listdir(reapdir)[0]), self.map_key, self.opt_key)
+            except dcm.DicomError:
+                return False, {}
             if not self.is_desired_item(df.opt):
                 log.info('ignoring     %s (non-matching opt-%s)', _id, self.opt)
                 return None, {}
         if success and reap_cnt == item['state']['images']:
-            metadata_map = dcm.pkg_series(_id, reapdir, self.map_key, self.opt_key, self.anonymize, self.timezone)
-            return True, metadata_map
+            try:
+                metadata_map = dcm.pkg_series(_id, reapdir, self.map_key, self.opt_key, self.anonymize, self.timezone, self.additional_metadata)
+            except dcm.DicomError:
+                return False, {}
+            else:
+                return True, metadata_map
         else:
             return False, {}
 
@@ -88,6 +98,7 @@ def update_arg_parser(ap):
     ap.add_argument('aec', help='remote AE title')
 
     ap.add_argument('-A', '--no-anonymize', dest='anonymize', action='store_false', help='do not anonymize patient name and birthdate')
+    ap.add_argument('--metadata', nargs=3, default=[], action='append', help='Additional metadata to package')
 
     return ap
 

reaper/util.py

@@ -61,7 +61,7 @@ def hrsize(size):
     return '%.0f%sB' % (size, 'Y')
 
 
-def object_metadata(obj, timezone, filename):
+def object_metadata(obj, timezone, filename, additional_metadata=None):
     # pylint: disable=missing-docstring
     metadata = {
         'session': {'timezone': timezone},
@@ -75,6 +75,10 @@ def object_metadata(obj, timezone, filename):
     metadata['file']['name'] = filename
     metadata['session']['subject'] = metadata.pop('subject', {})
     metadata['acquisition']['files'] = [metadata.pop('file', {})]
+    for md_group, md_group_info in (additional_metadata or {}).iteritems():
+        metadata.setdefault(md_group, {})
+        metadata[md_group].setdefault('metadata', {})
+        metadata[md_group]['metadata'].update(md_group_info)
     return metadata
 
 

test/lint.sh

@@ -6,9 +6,9 @@ unset CDPATH
 cd "$( dirname "${BASH_SOURCE[0]}" )/.."
 
 echo "Running pylint ..."
-pylint --reports=no "$@"
+pylint --reports=no reaper
 
 echo
 
 echo "Running pep8 ..."
-pep8 --max-line-length=150 --ignore=E402 "$@"
+pep8 --max-line-length=150 --ignore=E402 reaper

test/test.sh

@@ -29,7 +29,7 @@ RECEIVER_PID=$!
 # Fetch test data
 mkdir -p $TESTDATA_DIR
 if [ ! "$(ls -A $TESTDATA_DIR)" ]; then
-    curl -L https://github.com/scitran/testdata/archive/master.tar.gz | tar xz -C $TESTDATA_DIR --strip-components 1
+    curl -L https://github.com/scitran/testdata/archive/reaper-ci.tar.gz | tar xz -C $TESTDATA_DIR --strip-components 1
 fi