missing Images key

Author: vsoch

sendit/apps/main/tasks/get.py

@@ -125,7 +125,6 @@ def import_dicomdir(dicom_dir, run_get_identifiers=True):
  series_id = dcm.get('SeriesNumber')
  if series_id not in all_series:
  all_series.append(series_id)
-
  if study_date not in study_dates:
  study_dates[study_date] = 0
  study_dates[study_date] += 1
@@ -141,7 +140,6 @@ def import_dicomdir(dicom_dir, run_get_identifiers=True):
  message = "%s is flagged in %s: %s, skipping" %(dicom_uid, 
  flag_group,
  reason)
-
  batch = add_batch_warning(message,batch,quiet=True)
  message = "BurnedInAnnotation found for batch %s" %batch.uid
  if message not in messages:
@@ -155,13 +153,12 @@ def import_dicomdir(dicom_dir, run_get_identifiers=True):
 
  # Series Number and count of slices (images)
  if series_id is not None and series_id not in series:
- series[series_id] = {'SeriesNumber': series_id }
-
+ series[series_id] = {'SeriesNumber': series_id,
+ 'Images':1 }
  # Series Description
  description = dcm.get('SeriesDescription')
  if dcm.get('SeriesDescription') is not None:
  series[series_id]['SeriesDescription'] = description
-
  else:
  series[series_id]['Images'] +=1
 

sendit/apps/main/tasks/update.py

@@ -60,6 +60,7 @@
 
 from django.conf import settings
 import os
+import time
 from copy import deepcopy
 
 os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'sendit.settings')
@@ -108,7 +109,6 @@ def replace_identifiers(bid, run_upload_storage=False):
  '''
 
  batch.qa['ProcessStartTime'] = time.time()
-
  batch = Batch.objects.get(id=bid)
  batch_ids = BatchIdentifiers.objects.get(batch=batch) 
 
@@ -125,12 +125,10 @@ def replace_identifiers(bid, run_upload_storage=False):
  cleaned = clean_identifiers(ids=updated,
  default="KEEP",
  deid=deid)
-
  # Save progress
  batch_ids.cleaned = cleaned 
  batch_ids.updated = updated
  batch_ids.save()
- 
  # Get updated files
  dicom_files = batch.get_image_paths()
  output_folder = batch.get_path()
@@ -142,7 +140,6 @@ def replace_identifiers(bid, run_upload_storage=False):
  strip_sequences=True,
  remove_private=True) # force = True
  # save = True,
-
  # Get shared information
  aggregate = ["BodyPartExamined", "Modality", "StudyDescription"]
  shared_ids = get_shared_identifiers(dicom_files=updated_files, 
@@ -158,24 +155,19 @@ def replace_identifiers(bid, run_upload_storage=False):
 
  # S6M0<MRN-SUID>_<JITTERED-REPORT-DATE>_<ACCESSIONNUMBER-SUID>
  # Rename the dicom based on suid
-
  if item_id in updated:
  item_suid = updated[item_id]['item_id']
  dcm = dcm.rename(item_suid) # added to [prefix][dcm.name] 
  dcm.save()
-
  # If we don't have the id, don't risk uploading
  else:
  message = "%s for Image Id %s file read error: skipping." %(item_id, dcm.id)
  batch = add_batch_error(message,batch) 
  dcm.delete()
-
-
  except:
  message = "%s for Image Id %s not found in lookup: skipping." %(item_id, dcm.id)
  batch = add_batch_error(message,batch) 
  dcm.delete()
- 
  batch.qa['ProcessFinishTime'] = time.time()
 
  # We don't get here if the call above failed