def load_directories():
global directories
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# Get Import settings
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
if is_import_settings_defined():
directories = parse_settings_file(get_settings('import'))
else:
directories = {'inbox': '', 'imported': '', 'review': ''}
def __init__(self, *config):
if config:
config = config[0]
else:
# Read SQL configuration file
abs_file_path = get_settings('sql')
config = parse_settings_file(abs_file_path)
self.dbname = config['dbname']
cnx = psycopg2.connect(**config)
self.cnx = cnx
self.cursor = cnx.cursor()
self.tables = ['DVHs', 'Plans', 'Rxs', 'Beams', 'DICOM_Files']
def load_sql_settings():
global config
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# Get SQL settings
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
if is_sql_connection_defined():
config = parse_settings_file(get_settings('sql'))
if 'user' not in list(config):
config['user'] = ''
config['password'] = ''
if 'password' not in list(config):
config['password'] = ''
else:
config = {'host': 'localhost',
'dbname': 'dvh',
'port': '5432',
'user': '',
'password': ''}
def dicom_to_sql(start_path=None,
force_update=False,
move_files=True,
update_dicom_catalogue_table=True):
start_time = datetime.now()
print(str(start_time), 'Beginning import', sep=' ')
dicom_catalogue_update = []
# Read SQL configuration file
abs_file_path = get_settings('import')
import_settings = parse_settings_file(abs_file_path)
if start_path:
abs_file_path = os.path.join(SCRIPT_DIR, start_path)
import_settings['inbox'] = abs_file_path
sqlcnx = DVH_SQL()
file_paths = get_file_paths(import_settings['inbox'])
for uid in list(file_paths):
if is_uid_imported(uid):
print("The UID from the following files is already imported.")
if not force_update:
print(
"Must delete content associated with this UID from database before reimporting."
)
print(
"These files have been moved into the 'misc' folder within your 'imported' folder."
)
for file_type in FILE_TYPES:
print(file_paths[uid][file_type]['file_path'])
print("The UID is %s" % uid)
continue
else:
print("Force Update set to True. Processing with import.")
print(
"WARNING: This import may contain duplicate data already in the database."
)
dicom_catalogue_update.append(uid)
# Collect and print the file paths
plan_file = file_paths[uid]['rtplan']['latest_file']
struct_file = file_paths[uid]['rtstruct']['latest_file']
dose_file = file_paths[uid]['rtdose']['latest_file']
if IMPORT_LATEST_PLAN_ONLY:
print("plan file: %s" % plan_file)
else:
for f in file_paths[uid]['rtplan']['file_path']:
print("plan file: %s" % f)
print("struct file: %s" % struct_file)
print("dose file: %s" % dose_file)
# Process DICOM files into Python objects
plan, beams, dvhs, rxs = [], [], [], []
mp, ms, md = [], [], []
if plan_file:
mp = dicom.read_file(plan_file).ManufacturerModelName.lower()
if struct_file:
ms = dicom.read_file(struct_file).ManufacturerModelName.lower()
if dose_file:
md = dicom.read_file(dose_file).ManufacturerModelName.lower()
if 'gammaplan' in "%s %s %s" % (mp, ms, md):
print(
"Leksell Gamma Plan is not currently supported. Skipping import."
)
continue
if plan_file and struct_file and dose_file:
if IMPORT_LATEST_PLAN_ONLY:
plan = PlanRow(plan_file, struct_file, dose_file)
sqlcnx.insert_plan(plan)
else:
for f in file_paths[uid]['rtplan']['file_path']:
plan = PlanRow(f, struct_file, dose_file)
sqlcnx.insert_plan(plan)
else:
print(
'WARNING: Missing complete set of plan, struct, and dose files for uid %s'
% uid)
if not force_update:
print(
'WARNING: Skipping this import. If you wish to import an incomplete DICOM set, use Force Update'
)
print(
'WARNING: The current file will be moved to the misc folder with in your imported folder'
)
continue
if plan_file:
if not hasattr(dicom.read_file(plan_file), 'BrachyTreatmentType'):
if IMPORT_LATEST_PLAN_ONLY:
beams = BeamTable(plan_file)
sqlcnx.insert_beams(beams)
else:
for f in file_paths[uid]['rtplan']['file_path']:
sqlcnx.insert_beams(BeamTable(f))
if struct_file and dose_file:
dvhs = DVHTable(struct_file, dose_file)
setattr(dvhs, 'ptv_number', rank_ptvs_by_D95(dvhs))
sqlcnx.insert_dvhs(dvhs)
if plan_file and struct_file:
if IMPORT_LATEST_PLAN_ONLY:
rxs = RxTable(plan_file, struct_file)
sqlcnx.insert_rxs(rxs)
else:
for f in file_paths[uid]['rtplan']['file_path']:
sqlcnx.insert_rxs(RxTable(f, struct_file))
# get mrn for folder name, can't assume a complete set of dose, plan, struct files
mrn = []
if dose_file:
mrn = dicom.read_file(dose_file).PatientID
elif plan_file:
mrn = dicom.read_file(plan_file).PatientID
elif struct_file:
mrn = dicom.read_file(struct_file).PatientID
if mrn:
mrn = "".join(x for x in mrn
if x.isalnum()) # remove any special characters
else:
mrn = 'NoMRN'
# convert file_paths[uid] into a list of file paths
if move_files:
files_to_move = []
move_types = list(FILE_TYPES) + ['other']
for file_type in move_types:
files_to_move.extend(file_paths[uid][file_type]['file_path'])
new_folder = os.path.join(import_settings['imported'], mrn)
move_files_to_new_path(files_to_move, new_folder)
if plan_file:
plan_file = os.path.basename(plan_file)
if struct_file:
struct_file = os.path.basename(struct_file)
if dose_file:
dose_file = os.path.basename(dose_file)
if update_dicom_catalogue_table:
if not IMPORT_LATEST_PLAN_ONLY:
plan_file = ', '.join([
os.path.basename(fp)
for fp in file_paths[uid]['rtplan']['file_path']
])
update_dicom_catalogue(mrn, uid, new_folder, plan_file,
struct_file, dose_file)
# Move remaining files, if any
if move_files:
move_all_files(import_settings['imported'], import_settings['inbox'])
remove_empty_folders(import_settings['inbox'])
sqlcnx.close()
end_time = datetime.now()
print(str(end_time), 'Import complete', sep=' ')
total_time = end_time - start_time
seconds = total_time.seconds
m, s = divmod(seconds, 60)
h, m = divmod(m, 60)
if h:
print("This import took %dhrs %02dmin %02dsec to complete" % (h, m, s))
elif m:
print("This import took %02dmin %02dsec to complete" % (m, s))
else:
print("This import took %02dsec to complete" % s)
