missing Images key

pydicom · Oct 31, 2017 · 900a57f · 900a57f
1 parent eb57c5b
commit 900a57f
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Showing 2 changed files with 3 additions and 14 deletions.
diff --git a/sendit/apps/main/tasks/get.py b/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
 

diff --git a/sendit/apps/main/tasks/update.py b/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