populate psgRecordData with signal headers

some fields are commented out as their value is not yet clear
somnonetz · Mar 13, 2020 · 38dc470 · 38dc470
1 parent c232d4b
commit 38dc470
Showing 1 changed file with 33 additions and 13 deletions.
diff --git a/resources/catalog/somnonetz-pipeline/bin/extract_edf_header b/resources/catalog/somnonetz-pipeline/bin/extract_edf_header
@@ -13,30 +13,50 @@ if __name__ == "__main__":
     parser.add_argument('-host', required=True)
     parser.add_argument('-user', required=True)
     parser.add_argument('-pwd', required=True)
-    
+
     args = parser.parse_args()
     args.host = args.host.strip('/') # remove trailing slash from host as pyxnat fails to connect if it's present
 
     xnat = Interface(args.host, user=args.user, password=args.pwd)
     scan = xnat.select(f'/project/{args.project}/subject/{args.subject}/experiment/{args.session}/scan/psg')
     remote_edf = scan.resources().files().first()
     edf_path = remote_edf.get(f'./{remote_edf.label()}')
-    header = read_header(edf_path)
+    edf_header = read_header(edf_path)
 
     scan.insert(**{
         'scans': 'snet01:psgScanData',
-        'snet01:psgScanData/edfversion': header.version,
-        'snet01:psgScanData/patientid': header.local_patient_identification,
-        'snet01:psgScanData/localrecordid': header.local_recording_identification,
-        'snet01:psgScanData/recordingstartdate': header.startdate_of_recording,
-        'snet01:psgScanData/recordingstarttime': header.starttime_of_recording,
-        'snet01:psgScanData/numberofheaderbytes': header.number_of_bytes_in_header_record,
-        'snet01:psgScanData/reservedheaderfield': header.reserved,
-        'snet01:psgScanData/numberofdatarecords': header.number_of_data_records,
-        # 'snet01:psgScanData/durationofdatarecordseconds': header.duration_of_a_data_record,
-        'snet01:psgScanData/numberofsignalsindatarecord': header.number_of_signals,
+        'snet01:psgScanData/edfversion': edf_header.version,
+        'snet01:psgScanData/patientid': edf_header.local_patient_identification,
+        'snet01:psgScanData/localrecordid': edf_header.local_recording_identification,
+        'snet01:psgScanData/recordingstartdate': edf_header.startdate_of_recording,
+        'snet01:psgScanData/recordingstarttime': edf_header.starttime_of_recording,
+        'snet01:psgScanData/numberofheaderbytes': edf_header.number_of_bytes_in_header_record,
+        'snet01:psgScanData/reservedheaderfield': edf_header.reserved,
+        'snet01:psgScanData/numberofdatarecords': edf_header.number_of_data_records,
+        'snet01:psgScanData/durationofdatarecordseconds': edf_header.duration_of_a_data_record,
+        'snet01:psgScanData/numberofsignalsindatarecord': edf_header.number_of_signals,
         # 'snet01:psgScanData/psgdevice': '?',
-        # 'snet01:psgScanData/durationofrecordhours': header.duration_of_a_data_record,
+        'snet01:psgScanData/durationofrecordhours': edf_header.duration_of_a_data_record / 3600,
         # 'snet01:psgScanData/continuousdataflag': '0',
         # 'snet01:psgScanData/comment': '',
     })
+
+    for i, signal_header in enumerate(edf_header.signals):
+        scan.insert(**{
+            'scans': 'snet01:psgScanData',
+            'snet01:psgScanData/records/record/labeldevice': signal_header.label,
+            'snet01:psgScanData/records/record/labelstandard': signal_header.label,
+            'snet01:psgScanData/records/record/channelnumberdevice': i,
+            'snet01:psgScanData/records/record/channelnumberstandard': i,
+            # 'snet01:psgScanData/records/record/numberofchunks': ,
+            'snet01:psgScanData/records/record/samplingrate': signal_header.nr_of_samples_in_each_data_record / edf_header.duration_of_a_data_record,
+            'snet01:psgScanData/records/record/transducertype': signal_header.transducer_type,
+            'snet01:psgScanData/records/record/physicaldimension': signal_header.physical_dimension,
+            'snet01:psgScanData/records/record/physicalminimum': signal_header.physical_minimum,
+            'snet01:psgScanData/records/record/physicalmaximum': signal_header.physical_maximum,
+            'snet01:psgScanData/records/record/digitalminimum': signal_header.digital_minimum,
+            'snet01:psgScanData/records/record/digitalmaximum': signal_header.digital_maximum,
+            # 'snet01:psgScanData/records/record/prefiltering': ,
+            'snet01:psgScanData/records/record/samplesinrecord': signal_header.nr_of_samples_in_each_data_record,
+            'snet01:psgScanData/records/record/reserved': signal_header.reserved,
+        })