dbdicom 0.3.3__py3-none-any.whl → 0.3.5__py3-none-any.whl

dbdicom/register.py

@@ -1,14 +1,18 @@
 import os
 
 
-def add_instance(dbtree:list, instance, rel_path):
+class AmbiguousError(Exception):
+    pass
+
+
+def add_instance(dbtree:list, attr, rel_path):
     
     # Get patient and create if needed
-    pts = [pt for pt in dbtree if pt['PatientID']==instance['PatientID']]
+    pts = [pt for pt in sorted(dbtree, key=lambda pt: pt['PatientID']) if pt['PatientID']==attr['PatientID']]
     if pts==[]:
         pt = {
-            'PatientName': instance['PatientName'],
-            'PatientID': instance['PatientID'],
+            'PatientName': attr['PatientName'],
+            'PatientID': attr['PatientID'],
             'studies': [],
         }
         dbtree.append(pt)
@@ -16,13 +20,12 @@ def add_instance(dbtree:list, instance, rel_path):
         pt = pts[0]
     
     # Get study and create if needed
-    sts = [st for st in pt['studies'] if st['StudyInstanceUID']==instance['StudyInstanceUID']]
+    sts = [st for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']) if st['StudyInstanceUID']==attr['StudyInstanceUID']]
     if sts==[]:
         st = {
-            'StudyDescription': instance['StudyDescription'],
-            'StudyDate': instance['StudyDate'],
-            'StudyID': instance['StudyID'],
-            'StudyInstanceUID': instance['StudyInstanceUID'],
+            'StudyDescription': attr['StudyDescription'],
+            'StudyID': attr['StudyID'],
+            'StudyInstanceUID': attr['StudyInstanceUID'],
             'series': [],
         }
         pt['studies'].append(st)
@@ -30,12 +33,12 @@ def add_instance(dbtree:list, instance, rel_path):
         st = sts[0]
 
     # Get series and create if needed
-    srs = [sr for sr in st['series'] if sr['SeriesInstanceUID']==instance['SeriesInstanceUID']]
+    srs = [sr for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']) if sr['SeriesInstanceUID']==attr['SeriesInstanceUID']]
     if srs==[]:
         sr = {
-            'SeriesNumber': instance['SeriesNumber'],
-            'SeriesDescription': instance['SeriesDescription'],
-            'SeriesInstanceUID': instance['SeriesInstanceUID'],
+            'SeriesNumber': attr['SeriesNumber'],
+            'SeriesDescription': attr['SeriesDescription'],
+            'SeriesInstanceUID': attr['SeriesInstanceUID'],
             'instances': {},
         }
         st['series'].append(sr)
@@ -43,7 +46,7 @@ def add_instance(dbtree:list, instance, rel_path):
         sr = srs[0]
 
     # Add instance
-    sr['instances'][instance['InstanceNumber']] = rel_path
+    sr['instances'][attr['InstanceNumber']] = rel_path
 
     return dbtree
 
@@ -62,42 +65,42 @@ def files(dbtree, entity):
 def index(dbtree, entity):
     if isinstance(entity, str):
         idx = []
-        for pt in dbtree:
-            for st in pt['studies']:
-                for sr in st['series']:
+        for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
+            for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']):
+                for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                     idx += list(sr['instances'].values())
         return idx
     elif len(entity)==2:
-        patient_id = uid(dbtree, entity)
+        patient_id = entity[1]
         idx = []
-        for pt in dbtree:
+        for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
             if pt['PatientID'] == patient_id:
-                for st in pt['studies']:
-                    for sr in st['series']:
+                for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']):
+                    for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                         idx += list(sr['instances'].values())
                 return idx
     elif len(entity)==3:
         study_uid = uid(dbtree, entity)
         idx = []
-        for pt in dbtree:
-            for st in pt['studies']:
+        for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
+            for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']):
                 if st['StudyInstanceUID'] == study_uid:
-                    for sr in st['series']:
+                    for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                         idx += list(sr['instances'].values())
                     return idx
     elif len(entity)==4:
         series_uid = uid(dbtree, entity)
-        for pt in dbtree:
-            for st in pt['studies']:
-                for sr in st['series']:
+        for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
+            for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']):
+                for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                     if sr['SeriesInstanceUID'] == series_uid:
                         return list(sr['instances'].values())
                     
 
 def drop(dbtree, relpaths):
-    for pt in dbtree[:]:
-        for st in pt['studies'][:]:
-            for sr in st['series'][:]:
+    for pt in sorted(dbtree[:], key=lambda pt: pt['PatientID']):
+        for st in sorted(pt['studies'][:], key=lambda st: st['StudyInstanceUID']):
+            for sr in sorted(st['series'][:], key=lambda sr: sr['SeriesNumber']):
                 for nr, relpath in list(sr['instances'].items()):
                     if relpath in relpaths:
                         del sr['instances'][nr]
@@ -108,96 +111,24 @@ def drop(dbtree, relpaths):
     return dbtree
 
 
-# def entity(df, path, uid):# information entity from uid
-#     dbtree = tree(df)
-#     patient_idx = {}
-#     for pt in dbtree:
-#         patient_name = pt['PatientName']
-#         uid_patient = pt['PatientID']
-#         if patient_name in patient_idx:
-#             patient_idx[patient_name] += 1
-#         else:
-#             patient_idx[patient_name] = 0
-#         patient_desc = (patient_name, patient_idx[patient_name])
-#         if uid == uid_patient:
-#             return [path, patient_desc]
-        
-#         else:
-
-#             study_idx = {}
-#             for st in pt['studies']:
-#                 study_name = st['StudyDescription']
-#                 uid_study = st['StudyInstanceUID']
-#                 if study_name in study_idx:
-#                     study_idx[study_name] += 1
-#                 else:
-#                     study_idx[study_name] = 0
-#                 study_desc = (study_name, study_idx[study_name])
-#                 if uid == uid_study:
-#                     return [path, patient_desc, study_desc]
-                
-#                 else:
-
-#                     series_idx = {}
-#                     for sr in st['series']:
-#                         series_name = sr['SeriesDescription']
-#                         uid_series = sr['SeriesInstanceUID']
-#                         if series_name in series_idx:
-#                             series_idx[series_name] += 1
-#                         else:
-#                             series_idx[series_name] = 0
-#                         series_desc = (series_name, series_idx[series_name])
-#                         if uid == uid_series:
-#                             return [path, patient_desc, study_desc, series_desc]
-                        
-#     raise ValueError(f"No information entity with UID {uid} was found.")
-
 
 def uid(dbtree, entity): # uid from entity
     if len(entity)==2:
-        return _patient_uid(dbtree, entity)
+        return entity[1]
     if len(entity)==3:
-        return _study_uid(dbtree, entity)
+        return study_uid(dbtree, entity)
     if len(entity)==4:
-        return _series_uid(dbtree, entity)
-
-
-def _patient_uid(dbtree, patient):
-    patient = patient[1]
-    patients = {}
-    patient_idx = {}
-    for pt in dbtree:
-        patient_name = pt['PatientName']
-        uid_patient = pt['PatientID']
-        if patient_name in patient_idx:
-            patient_idx[patient_name] += 1
-        else:
-            patient_idx[patient_name] = 0
-        patient_desc = (patient_name, patient_idx[patient_name])
-        if patient == patient_desc:
-            return uid_patient
-        patients[patient_desc] = uid_patient
-    if isinstance(patient, str):
-        patient_list = [p for p in patients.keys() if p[0]==patient]
-        if len(patient_list) == 1:
-            return patients[(patient, 0)]
-        elif len(patient_list) > 1:
-            raise ValueError(
-                f"Multiple patients with name {patient}."
-                f"Please specify the index in the call to patient_uid(). "
-                f"For instance ({patient}, {len(patients)-1})'. "
-            )
-    
+        return series_uid(dbtree, entity)
     
 
-def _study_uid(dbtree, study):
-    uid_patient = _patient_uid(dbtree, study[:-1])
-    patient, study = study[1], study[2]
-    for pt in dbtree:
-        if pt['PatientID'] == uid_patient:
-            studies = {}
+def study_uid(dbtree, study):
+    patient_id, study = study[1], study[2]
+    for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
+        if pt['PatientID'] == patient_id:
+
+            uid_studies = {}
             study_idx = {}
-            for st in pt['studies']:
+            for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']):
                 study_desc = st['StudyDescription']
                 uid_study = st['StudyInstanceUID']
                 if study_desc in study_idx:
@@ -207,29 +138,31 @@ def _study_uid(dbtree, study):
                 study_desc = (study_desc, study_idx[study_desc])
                 if study == study_desc:
                     return uid_study
-                studies[study_desc] = uid_study
+                uid_studies[study_desc] = uid_study
+
             if isinstance(study, str):
-                studies_list = [s for s in studies.keys() if s[0]==study]
+                studies_list = [s for s in uid_studies.keys() if s[0]==study]
                 if len(studies_list) == 1:
-                    return studies[(study, 0)]
+                    return uid_studies[(study, 0)]
                 elif len(studies_list) > 1:
-                    raise ValueError(
-                        f"Multiple studies with name {study}."
-                        f"Please specify the index in the call to study_uid(). "
-                        f"For instance ({study}, {len(studies)-1})'. "
+                    raise AmbiguousError(
+                        f"Multiple studies with name {study}. "
+                        f"Please specify the index along with the description. "
+                        f"For instance ({study}, {len(uid_studies)-1})'. "
                     )
-            raise ValueError(f"Study {study} not found in patient {patient}.")
+            raise ValueError(f"Study {study} not found in patient {patient_id}.")
 
 
-def _series_uid(dbtree, series): # absolute path to series
-    uid_study = _study_uid(dbtree, series[:-1])
+def series_uid(dbtree, series): # absolute path to series
+    uid_study = study_uid(dbtree, series[:-1])
     study, sery = series[2], series[3]
-    for pt in dbtree:
-        for st in pt['studies']:
+    for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
+        for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']):
             if st['StudyInstanceUID'] == uid_study:
+
                 series = {}
                 series_idx = {}
-                for sr in st['series']:
+                for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                     series_desc = sr['SeriesDescription']
                     uid_series = sr['SeriesInstanceUID']
                     if series_desc in series_idx:
@@ -240,160 +173,75 @@ def _series_uid(dbtree, series): # absolute path to series
                     if sery == series_desc:
                         return uid_series
                     series[series_desc] = uid_series
+
                 if isinstance(sery, str):
                     series_list = [s for s in series.keys() if s[0]==sery]
                     if len(series_list) == 1:
                         return series[(sery, 0)]
                     elif len(series_list) > 1:
-                        raise ValueError(
-                            f"Multiple series with name {sery}."
-                            f"Please specify the index in the call to series_uid(). "
+                        raise AmbiguousError(
+                            f"Multiple series with name {sery}. "
+                            f"Please specify the index along with the description. "
                             f"For instance ({sery}, {len(series)-1})'. "
                         )
                 raise ValueError(f"Series {sery} not found in study {study}.")
 
 
 def patients(dbtree, database, name=None, contains=None, isin=None):
-    simplified_patients = []
-    patients = []
-    patient_idx = {}
-    for pt in dbtree:
-        patient_name = pt['PatientName']
-        if patient_name in patient_idx:
-            patient_idx[patient_name] += 1
-        else:
-            patient_idx[patient_name] = 0
-        patients.append((patient_name, patient_idx[patient_name]))
-    for patient in patients:
-        if patient_idx[patient[0]] == 0:
-            simplified_patients.append(patient[0])
-        else:
-            simplified_patients.append(patient)
-    if name is not None:
-        patients_result = []
-        for s in simplified_patients:
-            if isinstance(s, str):
-                if s == name:
-                    patients_result.append(s)
-            elif s[0] == name: 
-                patients_result.append(s)
-        return [[database, p] for p in patients_result]
-    elif contains is not None:
-        patients_result = []
-        for s in simplified_patients:
-            if isinstance(s, str):
-                if contains in s:
-                    patients_result.append(s)
-            elif contains in s[0]: 
-                patients_result.append(s)
-        return [[database, p] for p in patients_result]
-    elif isin is not None:
-        patients_result = []
-        for s in simplified_patients:
-            if isinstance(s, str):
-                if s in isin:
-                    patients_result.append(s)
-            elif s[0] in isin: 
-                patients_result.append(s)
-        return [[database, p] for p in patients_result]
-    else:
-        return [[database, p] for p in simplified_patients]
 
-
-def studies(dbtree, pat, name=None, contains=None, isin=None):
-    database, patient = pat[0], pat[1]
-    patient_as_str = isinstance(patient, str)
-    if patient_as_str:
-        patient = (patient, 0)
-    simplified_studies = []
-    patient_idx = {}
-    for pt in dbtree:
+    patients = []
+    for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
         patient_name = pt['PatientName']
-        if patient_name in patient_idx:
-            patient_idx[patient_name] += 1
-        else:
-            patient_idx[patient_name] = 0
-        if patient[0] == patient_name:
-            if patient_as_str:
-                if patient_idx[patient_name] > 0:
-                    raise ValueError(
-                        f"Multiple patients named {patient_name}. "
-                        "Please provide an index along with the patient name."
-                    )
-        if patient == (patient_name, patient_idx[patient_name]):
-            studies = []
+        append = True
+        if name is not None:
+            append = append and (patient_name==name)
+        if contains is not None:
+            append = append and (contains in patient_name)
+        if isin is not None:
+            append = append and (patient_name in isin)
+        if append:
+            patients.append(pt['PatientID'])
+
+    return [[database, p] for p in patients]
+
+
+def studies(dbtree, pat, desc=None, contains=None, isin=None):
+    database, patient_id = pat[0], pat[1]
+    studies = []
+    for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
+        if pt['PatientID'] == patient_id:
             study_idx = {}
-            for st in pt['studies']:
+            for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']):
                 study_desc = st['StudyDescription']
                 if study_desc in study_idx:
                     study_idx[study_desc] += 1
                 else:
                     study_idx[study_desc] = 0
                 studies.append((study_desc, study_idx[study_desc]))
-            for study in studies:
-                if study_idx[study[0]] == 0:
-                    simplified_studies.append(study[0])
-                else:
-                    simplified_studies.append(study)
-            if not patient_as_str:
-                break
-    if name is not None:    
-        studies_result = []
-        for s in simplified_studies:
-            if isinstance(s, str):
-                if s == name:
-                    studies_result.append(s)
-            elif s[0] == name: 
-                studies_result.append(s)
-        return [[database, patient, study] for study in studies_result]
-    elif contains is not None:
-        studies_result = []
-        for s in simplified_studies:
-            if isinstance(s, str):
-                if contains in s:
-                    studies_result.append(s)
-            elif contains in s[0]: 
-                studies_result.append(s)
-        return [[database, patient, study] for study in studies_result]
-    elif isin is not None:
-        studies_result = []
-        for s in simplified_studies:
-            if isinstance(s, str):
-                if s in isin:
-                    studies_result.append(s)
-            elif s[0] in isin: 
-                studies_result.append(s)
-        return [[database, patient, study] for study in studies_result]
-    else:
-        return [[database, patient, study] for study in simplified_studies]
+
+    # Apply filters
+    if desc is not None:   
+        studies = [s for s in studies if s[0]==desc] 
+    if contains is not None:
+        studies = [s for s in studies if contains in s[0]]
+    if isin is not None:
+        studies = [s for s in studies if s[0] in isin]
+
+    # Return result
+    return [[database, patient_id, study] for study in studies]
 
 
 
-def series(dbtree, stdy, name=None, contains=None, isin=None):
-    database, patient, study = stdy[0], stdy[1], stdy[2]
-    patient_as_str = isinstance(patient, str)
-    if patient_as_str:
-        patient = (patient, 0)
+def series(dbtree, stdy, desc=None, contains=None, isin=None):
+    database, patient_id, study = stdy[0], stdy[1], stdy[2]
     study_as_str = isinstance(study, str)
     if study_as_str:
         study = (study, 0)
-    simplified_series = []
-    patient_idx = {}
-    for pt in dbtree:
-        patient_name = pt['PatientName']
-        if patient_name in patient_idx:
-            patient_idx[patient_name] += 1
-        else:
-            patient_idx[patient_name] = 0
-        if patient[0] == patient_name:
-            if patient_as_str:
-                if patient_idx[patient_name] > 0:
-                    raise ValueError(
-                        f"Multiple patients named {patient_name}. Please provide an index along with the patient name."
-                    )
-        if patient == (patient_name, patient_idx[patient_name]):
+    series = []
+    for pt in sorted(dbtree, key=lambda pt: pt['PatientID']):
+        if pt['PatientID'] == patient_id:
             study_idx = {}
-            for st in pt['studies']:
+            for st in sorted(pt['studies'], key=lambda st: st['StudyInstanceUID']):
                 study_desc = st['StudyDescription']
                 if study_desc in study_idx:
                     study_idx[study_desc] += 1
@@ -402,126 +250,63 @@ def series(dbtree, stdy, name=None, contains=None, isin=None):
                 if study[0] == study_desc:
                     if study_as_str:
                         if study_idx[study_desc] > 0:
-                            raise ValueError(
-                                f"Multiple studies named {study_desc} in patient {patient_name}. Please provide an index along with the study description."
+                            raise AmbiguousError(
+                                f"Multiple studies named {study_desc} in patient {patient_id}. Please provide an index along with the study description."
                             )
                 if study == (study_desc, study_idx[study_desc]):
-                    series = []
                     series_idx = {}
-                    for sr in st['series']:
+                    for sr in sorted(st['series'], key=lambda sr: sr['SeriesNumber']):
                         series_desc = sr['SeriesDescription']
                         if series_desc in series_idx:
                             series_idx[series_desc] += 1
                         else:
                             series_idx[series_desc] = 0
                         series.append((series_desc, series_idx[series_desc]))
-                    for sery in series:
-                        if series_idx[sery[0]] == 0:
-                            simplified_series.append(sery[0])
-                        else:
-                            simplified_series.append(sery)
-                    if not (patient_as_str or study_as_str):
+                    if not study_as_str:
                         break
-    if name is not None:    
-        series_result = []
-        for s in simplified_series:
-            if isinstance(s, str):
-                if s == name:
-                    series_result.append(s)
-            elif s[0] == name: 
-                series_result.append(s)
-        return [[database, patient, study, series] for series in series_result]
-    elif contains is not None:    
-        series_result = []
-        for s in simplified_series:
-            if isinstance(s, str):
-                if contains in s:
-                    series_result.append(s)
-            elif contains in s[0]: 
-                series_result.append(s)
-        return [[database, patient, study, series] for series in series_result]
-    elif isin is not None:    
-        series_result = []
-        for s in simplified_series:
-            if isinstance(s, str):
-                if s in isin:
-                    series_result.append(s)
-            elif s[0] in isin: 
-                series_result.append(s)
-        return [[database, patient, study, series] for series in series_result]
-    else:
-        return [[database, patient, study, series] for series in simplified_series] 
-    
 
+    # Apply filters (if any)
+    if desc is not None:    
+        series = [s for s in series if s[0]==desc]
+    if contains is not None:    
+        series = [s for s in series if contains in s[0]]
+    if isin is not None:   
+        series = [s for s in series if s[0] in isin] 
 
+    # Return result
+    return [[database, patient_id, study, s] for s in series] 
+    
 
-def append(dbtree, parent, child_name): 
-    if len(parent) == 1:
-        return _new_patient(dbtree, parent, child_name)
-    elif len(parent) == 2:
-        return _new_study(dbtree, parent, child_name)
-    elif len(parent) == 3:
-        return _new_series(dbtree, parent, child_name)
 
-def _new_patient(dbtree, database, patient_name):
-    # Count the number of series with the same description
-    desc = patient_name if isinstance(patient_name, str) else patient_name[0]
-    patients_in_db = patients(dbtree, database, name=desc)
-    cnt = len(patients_in_db)
-    if cnt==0:
-        return [database, desc]
-    else:
-        return [database, (desc, cnt+1)]
+# def append(dbtree, parent, child_name): 
+#     if len(parent) == 1:
+#         return _new_patient(dbtree, parent, child_name)
+#     elif len(parent) == 2:
+#         return _new_study(dbtree, parent, child_name)
+#     elif len(parent) == 3:
+#         return _new_series(dbtree, parent, child_name)
+
+# def _new_patient(dbtree, database, patient_id):
+#     if patient_id in patients(dbtree, database):
+#         raise ValueError(
+#             f"Cannot create a new patient with id {patient_id}."
+#             f"The ID is already taken."
+#         )
+#     return [database, patient_id]
     
-def _new_study(dbtree, patient, study_name): #len(patient)=2
-    # Count the number of series with the same description
-    desc = study_name if isinstance(study_name, str) else study_name[0]
-    studies_in_patient = studies(dbtree, patient, name=desc)
-    cnt = len(studies_in_patient)
-    if cnt==0:
-        return patient + [desc]
-    else:
-        return patient + [(desc, cnt+1)]
+# def new_study(dbtree, patient, study): #len(patient)=2
+#     desc = study if isinstance(study, str) else study[0]
+#     studies_in_patient = studies(dbtree, patient, desc=desc)
+#     cnt = len(studies_in_patient)
+#     return patient + [(desc, cnt)]
     
-def _new_series(dbtree, study, series_name): #len(study)=3
-    # Count the number of series with the same description
-    desc = series_name if isinstance(series_name, str) else series_name[0]
-    series_in_study = series(dbtree, study, name=desc)
-    cnt = len(series_in_study)
-    if cnt==0:
-        return study + [desc]
-    else:
-        return study + [(desc, cnt+1)]
+# def new_series(dbtree, study, sery): #len(study)=3
+#     desc = sery if isinstance(sery, str) else sery[0]
+#     series_in_study = series(dbtree, study, desc=desc)
+#     cnt = len(series_in_study)
+#     return study + [(desc, cnt)]
 
 
-# def uid_tree(df, path, depth=3):
-
-#     dbtree = summary(df)
-    
-#     database = {'uid': path}
-#     database['patients'] = []
-#     for pat in dbtree:
-#         patient = {'uid': pat['PatientID']}
-#         database['patients'].append(patient)
-#         if depth >= 1:
-#             df_patient = df[df.PatientID == pat['PatientID']]
-#             patient['key'] = df_patient.index[0] 
-#             patient['studies'] = []
-#             for stdy in pat['studies']:
-#                 study = {'uid': stdy['StudyInstanceUID']}
-#                 patient['studies'].append(study)
-#                 if depth >= 2:
-#                     df_study = df_patient[df_patient.StudyInstanceUID == stdy['StudyInstanceUID']]
-#                     study['key'] = df_study.index[0]
-#                     study['series'] = []
-#                     for sery in stdy['series']:
-#                         series = {'uid': sery['SeriesInstanceUID']}
-#                         study['series'].append(series)
-#                         if depth == 3:
-#                             df_series = df_study[df_study.SeriesInstanceUID == sery['SeriesInstanceUID']]
-#                             series['key'] = df_series.index[0]
-#     return database
-
 
 def print_tree(dbtree):
     tree = summary(dbtree)
@@ -533,76 +318,32 @@ def print_tree(dbtree):
                 print(f"    Series: ({s[0]}, {s[1]})")
 
 
-# def summary(df):
-#     # A human-readable summary tree
-
-#     df = _prep(df)
-#     summary = {}
-
-#     patient_idx = {}
-#     for uid_patient in df.PatientID.dropna().unique():
-#         df_patient = df[df.PatientID == uid_patient]
-#         patient_name = df_patient.PatientName.values[0]
-#         if patient_name in patient_idx:
-#             patient_idx[patient_name] += 1
-#         else:
-#             patient_idx[patient_name] = 0
-#         summary[patient_name, patient_idx[patient_name]] = {}
-
-#         study_idx = {}
-#         for uid_study in df_patient.StudyInstanceUID.dropna().unique():
-#             df_study = df_patient[df_patient.StudyInstanceUID == uid_study]
-#             study_desc = df_study.StudyDescription.values[0]
-#             if study_desc in study_idx:
-#                 study_idx[study_desc] += 1
-#             else:
-#                 study_idx[study_desc] = 0
-#             summary[patient_name, patient_idx[patient_name]][study_desc, study_idx[study_desc]] = []
-
-#             series_idx = {}
-#             for uid_sery in df_study.SeriesInstanceUID.dropna().unique():
-#                 df_series = df_study[df_study.SeriesInstanceUID == uid_sery]
-#                 series_desc = df_series.SeriesDescription.values[0]
-#                 if series_desc in series_idx:
-#                     series_idx[series_desc] += 1
-#                 else:
-#                     series_idx[series_desc] = 0
-#                 summary[patient_name, patient_idx[patient_name]][study_desc, study_idx[study_desc]].append((series_desc, series_idx[series_desc]))
-    
-#     return summary
-
-
 def summary(dbtree):
     # A human-readable summary tree
 
     summary = {}
 
-    patient_idx = {}
-    for patient in dbtree:
-        patient_name = patient['PatientName']
-        if patient_name in patient_idx:
-            patient_idx[patient_name] += 1
-        else:
-            patient_idx[patient_name] = 0
-        summary[patient_name, patient_idx[patient_name]] = {}
+    for patient in sorted(dbtree, key=lambda pt: pt['PatientID']):
+        pat_id, pat_name = patient['PatientID'], patient['PatientName']
+        summary[pat_id, pat_name] = {}
 
         study_idx = {}
-        for study in patient['studies']:
+        for study in sorted(patient['studies'], key=lambda st: st['StudyInstanceUID']):
             study_desc = study['StudyDescription']
             if study_desc in study_idx:
                 study_idx[study_desc] += 1
             else:
                 study_idx[study_desc] = 0
-            summary[patient_name, patient_idx[patient_name]][study_desc, study_idx[study_desc]] = []
+            summary[pat_id, pat_name][study_desc, study_idx[study_desc]] = []
 
             series_idx = {}
-            for series in study['series']:
+            for series in sorted(study['series'], key=lambda sr: sr['SeriesNumber']):
                 series_desc = series['SeriesDescription']
                 if series_desc in series_idx:
                     series_idx[series_desc] += 1
                 else:
                     series_idx[series_desc] = 0
-                summary[patient_name, patient_idx[patient_name]][study_desc, study_idx[study_desc]].append((series_desc, series_idx[series_desc]))
+                summary[pat_id, pat_name][study_desc, study_idx[study_desc]].append((series_desc, series_idx[series_desc]))
     
     return summary