class QuerySQL:
def __init__(self, table_name, condition_str, unique=False):
table_name = table_name.lower()
if table_name in {'beams', 'dvhs', 'plans', 'rxs'}:
self.table_name = table_name
self.condition_str = condition_str
self.cnx = DVH_SQL()
# column names, use as property names
column_cursor = self.cnx.get_column_names(table_name)
for row in column_cursor:
column = str(row).strip()
if column not in {'roi_coord_string, distances_to_ptv, dth_string'}:
self.cursor = self.cnx.query(self.table_name,
column,
self.condition_str)
if unique:
rtn_list = get_unique_list(self.cursor_to_list())
else:
rtn_list = self.cursor_to_list()
setattr(self, column, rtn_list)
else:
print('Table name in valid. Please select from Beams, DVHs, Plans, or Rxs.')
def cursor_to_list(self):
rtn_list = []
for row in self.cursor:
if isinstance(row[0], (int, long, float)):
rtn_list.append(row[0])
else:
rtn_list.append(str(row[0]))
return rtn_list
def __init__(self, uid=None, dvh_condition=None):
"""
This class will retrieve DVHs and other data in the DVH SQL table meeting the given constraints,
it will also parse the DVH_string into python lists and retrieve the associated Rx dose
:param uid: a list of allowed study_instance_uids in data set
:param dvh_condition: a string in SQL syntax applied to a DVH Table query
"""
if uid:
constraints_str = "study_instance_uid in ('%s')" % "', '".join(uid)
if dvh_condition:
constraints_str = " and " + constraints_str
else:
constraints_str = ''
if dvh_condition:
constraints_str = "(%s)%s" % (dvh_condition, constraints_str)
self.query = dvh_condition
else:
self.query = ''
cnx = DVH_SQL()
# Get DVH data from SQL
dvh_data = QuerySQL('DVHs', constraints_str)
for key, value in dvh_data.__dict__.items():
if not key.startswith("__"):
setattr(self, key, value)
# Add these properties to dvh_data since they aren't in the DVHs SQL table
self.count = len(self.mrn)
self.rx_dose = []
self.bin_count = 0
for value in self.dvh_string:
current_dvh_str = np.array(str(value).split(','))
current_size = np.size(current_dvh_str)
if current_size > self.bin_count:
self.bin_count = current_size
self.dvh = np.zeros([self.bin_count, self.count])
# Get needed values not in DVHs table
for i in range(self.count):
# Get Rx Doses
condition = "mrn = '%s' and study_instance_uid = '%s'" % (
self.mrn[i], self.study_instance_uid[i])
rx_dose_cursor = cnx.query('Plans', 'rx_dose', condition)
self.rx_dose.append(rx_dose_cursor[0][0])
# Process dvh_string to numpy array, and pad with zeros at the end
# so that all dvhs are the same length
current_dvh = np.array(self.dvh_string[i].split(','),
dtype='|S4').astype(np.float)
current_dvh_max = np.max(current_dvh)
if current_dvh_max > 0:
current_dvh = np.divide(current_dvh, current_dvh_max)
zero_fill = np.zeros(self.bin_count - len(current_dvh))
self.dvh[:, i] = np.concatenate((current_dvh, zero_fill))
def get_physician_from_uid(uid):
cnx = DVH_SQL()
condition = "study_instance_uid = '" + uid + "'"
results = cnx.query('Plans', 'physician', condition)
if len(results) > 1:
print('Warning: multiple plans with this study_instance_uid exist')
return str(results[0][0])
def __init__(self, **kwargs):
if 'uid' in kwargs:
study_instance_uid = kwargs['uid']
db_constraints_list = []
for i in range(0, len(study_instance_uid)):
db_constraints_list.append(study_instance_uid[i])
uid_constraints_str = "study_instance_uid in ('"
uid_constraints_str += "', '".join(db_constraints_list)
uid_constraints_str += "')"
if 'dvh_condition' in kwargs and kwargs['dvh_condition']:
uid_constraints_str = " and " + uid_constraints_str
else:
uid_constraints_str = ''
if 'dvh_condition' in kwargs and kwargs['dvh_condition']:
uid_constraints_str = '(' + kwargs['dvh_condition'] + ')' + uid_constraints_str
self.query = kwargs['dvh_condition']
else:
self.query = ''
if 'uncategorized' in kwargs:
if kwargs['uncategorized']:
self.uncategorized = True
else:
self.uncategorized = False
else:
self.uncategorized = False
cnx = DVH_SQL()
# Get DVH data from SQL
dvh_data = QuerySQL('DVHs', uid_constraints_str)
for key, value in dvh_data.__dict__.items():
if not key.startswith("__"):
setattr(self, key, value)
# Add this properties to dvh_data since they aren't in the DVHs SQL table
self.count = len(self.mrn)
setattr(self, 'rx_dose', [])
self.bin_count = 0
for value in self.dvh_string:
current_dvh_str = np.array(str(value).split(','))
current_size = np.size(current_dvh_str)
if current_size > self.bin_count:
self.bin_count = current_size
setattr(self, 'dvh', np.zeros([self.bin_count, self.count]))
# Get needed values not in DVHs table
for i in range(0, self.count):
# Get Rx Doses
condition = "mrn = '" + self.mrn[i]
condition += "' and study_instance_uid = '"
condition += str(self.study_instance_uid[i]) + "'"
rx_dose_cursor = cnx.query('Plans', 'rx_dose', condition)
self.rx_dose.append(rx_dose_cursor[0][0])
# Process dvh_string to numpy array, and pad with zeros at the end
# so that all dvhs are the same length
current_dvh = np.array(self.dvh_string[i].split(','), dtype='|S4').astype(np.float)
if np.max(current_dvh) > 0:
current_dvh = np.divide(current_dvh, np.max(current_dvh))
zero_fill = np.zeros(self.bin_count - len(current_dvh))
self.dvh[:, i] = np.concatenate((current_dvh, zero_fill))