def recalculate_total_mu(*custom_condition):
if custom_condition:
custom_condition = " AND " + custom_condition[0]
else:
custom_condition = ''
# Get entire table
beam_data = QuerySQL('Beams', "mrn != ''" + custom_condition)
cnx = DVH_SQL()
plan_mus = {}
for i in range(0, len(beam_data.study_instance_uid)):
uid = beam_data.study_instance_uid[i]
beam_mu = beam_data.beam_mu[i]
fxs = float(beam_data.fx_count[i])
if uid not in list(plan_mus):
plan_mus[uid] = 0.
plan_mus[uid] += beam_mu * fxs
for uid in list(plan_mus):
cnx.update('Plans', 'total_mu', str(round(plan_mus[uid], 1)),
"study_instance_uid = '%s'" % uid)
cnx.close()
def validate_sql_connection(*config, **kwargs):
if config:
try:
cnx = DVH_SQL(config[0])
cnx.close()
valid = True
except:
valid = False
else:
try:
cnx = DVH_SQL()
cnx.close()
valid = True
except:
valid = False
if not kwargs or ('verbose' in kwargs and kwargs['verbose']):
if valid:
print("SQL DB is alive!")
else:
print("Connection to SQL DB could not be established.")
if not is_sql_connection_defined():
print(
"ERROR: SQL settings are not yet defined. Please run:\n",
" $ dvh settings --sql",
sep="")
return valid
def validate_sql_connection(config=None, verbose=False):
"""
:param config: a dict with keys 'host', 'dbname', 'port' and optionally 'user' and 'password'
:param verbose: boolean indicating if cmd line printing should be performed
:return:
"""
valid = True
if config:
try:
cnx = DVH_SQL(config)
cnx.close()
except:
valid = False
else:
try:
cnx = DVH_SQL()
cnx.close()
except:
valid = False
if verbose:
if valid:
print("SQL DB is alive!")
else:
print("Connection to SQL DB could not be established.")
if not is_sql_connection_defined():
print(
"ERROR: SQL settings are not yet defined. Please run:\n",
" $ dvh settings --sql",
sep="")
return valid
def reinitialize_roi_categories_in_database():
roi_map = DatabaseROIs()
dvh_data = QuerySQL('DVHs', "mrn != ''")
cnx = DVH_SQL()
for i in range(0, len(dvh_data.roi_name)):
uid = dvh_data.study_instance_uid[i]
physician = get_physician_from_uid(uid)
roi_name = dvh_data.roi_name[i]
new_physician_roi = roi_map.get_physician_roi(physician, roi_name)
new_institutional_roi = roi_map.get_institutional_roi(
physician, roi_name)
print(i,
physician,
new_institutional_roi,
new_physician_roi,
roi_name,
sep=' ')
condition = "study_instance_uid = '" + uid + "'" + "and roi_name = '" + roi_name + "'"
cnx.update('DVHs', 'physician_roi', new_physician_roi, condition)
cnx.update('DVHs', 'institutional_roi', new_institutional_roi,
condition)
cnx.close()
def beam_complexities(*condition):
if condition:
condition = condition[0]
cnx = DVH_SQL()
uids = cnx.get_unique_values('Beams',
'study_instance_uid',
condition,
return_empty=True)
for uid in uids:
beam_complexity(cnx, uid)
cnx.close()
def update_all_plan_toxicity_grades(*condition):
if condition:
condition = condition[0]
cnx = DVH_SQL()
uids = cnx.get_unique_values('Plans',
'study_instance_uid',
condition,
return_empty=True)
for uid in uids:
update_plan_toxicity_grades(uid)
cnx.close()
def recalculate_ages(*custom_condition):
if custom_condition:
custom_condition = " AND " + custom_condition[0]
else:
custom_condition = ''
dvh_data = QuerySQL('Plans', "mrn != ''" + custom_condition)
cnx = DVH_SQL()
for i in range(0, len(dvh_data.mrn)):
mrn = dvh_data.mrn[i]
uid = dvh_data.study_instance_uid[i]
sim_study_date = dvh_data.sim_study_date[i].split('-')
birth_date = dvh_data.birth_date[i].split('-')
try:
birth_year = int(birth_date[0])
birth_month = int(birth_date[1])
birth_day = int(birth_date[2])
birth_date_obj = datetime(birth_year, birth_month, birth_day)
sim_study_year = int(sim_study_date[0])
sim_study_month = int(sim_study_date[1])
sim_study_day = int(sim_study_date[2])
sim_study_date_obj = datetime(sim_study_year, sim_study_month,
sim_study_day)
if sim_study_date == '1800-01-01':
age = '(NULL)'
else:
age = relativedelta(sim_study_date_obj, birth_date_obj).years
condition = "study_instance_uid = '" + uid + "'"
cnx.update('Plans', 'age', str(age), condition)
except:
print("Update Failed for",
mrn,
"sim date:",
sim_study_date,
"birthdate",
birth_date,
sep=' ')
cnx.close()
def update_uncategorized_rois_in_database():
roi_map = DatabaseROIs()
dvh_data = QuerySQL('DVHs', "physician_roi = 'uncategorized'")
cnx = DVH_SQL()
for i in range(len(dvh_data.roi_name)):
uid = dvh_data.study_instance_uid[i]
mrn = dvh_data.mrn[i]
physician = get_physician_from_uid(uid)
roi_name = dvh_data.roi_name[i]
new_physician_roi = roi_map.get_physician_roi(physician, roi_name)
new_institutional_roi = roi_map.get_institutional_roi(physician, roi_name)
if new_physician_roi != 'uncategorized':
print(mrn, physician, new_institutional_roi, new_physician_roi, roi_name, sep=' ')
condition = "study_instance_uid = '" + uid + "'" + "and roi_name = '" + roi_name + "'"
cnx.update('DVHs', 'physician_roi', new_physician_roi, condition)
cnx.update('DVHs', 'institutional_roi', new_institutional_roi, condition)
cnx.close()
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)