def update_data(self, load_saved_dvh_data=False):
wait = wx.BusyCursor()
tables = ['Plans', 'Rxs', 'Beams']
if hasattr(self.dvh, 'study_instance_uid'):
if not load_saved_dvh_data:
condition_str = "study_instance_uid in ('%s')" % "','".join(
self.dvh.study_instance_uid)
self.data = {
key: QuerySQL(key, condition_str)
for key in tables
}
else:
self.data = {key: None for key in tables}
del wait
if hasattr(self.dvh, 'study_instance_uid'):
wait = wx.BusyCursor()
self.stats_data = StatsData(self.dvh, self.data)
self.regression.stats_data = self.stats_data
self.control_chart.stats_data = self.stats_data
try:
self.regression.update_combo_box_choices()
except ValueError:
# TODO: Print error in GUI
pass
self.control_chart.update_combo_box_y_choices()
del wait
def update_data(self, load_saved_dvh_data=False, group_2_only=False):
wx.BeginBusyCursor()
tables = ['Plans', 'Rxs', 'Beams']
for grp, grp_data in self.group_data.items():
if not(grp == 1 and group_2_only) or grp == 2:
if hasattr(grp_data['dvh'], 'study_instance_uid'):
if not load_saved_dvh_data:
condition_str = "study_instance_uid in ('%s')" % "','".join(
grp_data['dvh'].study_instance_uid)
grp_data['data'] = {key: QuerySQL(key, condition_str) for key in tables}
grp_data['stats_data'] = StatsData(grp_data['dvh'], grp_data['data'], group=grp)
else:
grp_data['data'] = {key: None for key in tables}
grp_data['stats_data'] = None
if self.group_data[2]['stats_data']:
sync_variables_in_stats_data_objects(self.group_data[1]['stats_data'],
self.group_data[2]['stats_data'])
self.time_series.update_data(self.group_data)
self.control_chart.update_data(self.group_data)
self.correlation.set_data(self.group_data)
self.regression.update_combo_box_choices()
self.radbio.update_dvh_data(self.group_data)
wx.EndBusyCursor()
def update_uncategorized_rois_in_database():
roi_map = DatabaseROIs()
dvh_data = QuerySQL('DVHs', "physician_roi = 'uncategorized'")
with DVH_SQL() as cnx:
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)
def __init__(self, uid=None, dvh_condition=None, dvh_bin_width=5):
"""
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
:param dvh_bin_width: retrieve every nth value from dvh_string in SQL
:type dvh_bin_width: int
"""
self.dvh_bin_width = dvh_bin_width
if uid:
constraints_str = "study_instance_uid in ('%s')" % "', '".join(uid)
if dvh_condition:
constraints_str = "(%s) and %s" % (dvh_condition,
constraints_str)
else:
constraints_str = ''
# Get DVH data from SQL and set as attributes
dvh_data = QuerySQL('DVHs', constraints_str)
if dvh_data.mrn:
ignored_keys = {
'cnx', 'cursor', 'table_name', 'constraints_str',
'condition_str'
}
self.keys = []
for key, value in dvh_data.__dict__.items():
if not key.startswith("__") and key not in ignored_keys:
if key == 'dvh_string':
dvh_split = [
dvh.split(',')[::self.dvh_bin_width]
for i, dvh in enumerate(value)
]
setattr(self, key, value)
if '_string' not in key:
self.keys.append(key)
# Move mrn to beginning of self.keys
if 'mrn' in self.keys:
self.keys.pop(self.keys.index('mrn'))
self.keys.insert(0, 'mrn')
# uid passed into DVH init is a unique list for querying and it is not in order of query results
self.uid = self.study_instance_uid
# Add these properties to dvh_data since they aren't in the DVHs SQL table
self.count = len(self.mrn)
self.study_count = len(set(self.uid))
self.rx_dose = self.get_plan_values('rx_dose')
self.sim_study_date = self.get_plan_values('sim_study_date')
self.keys.append('rx_dose')
self.endpoints = {'data': None, 'defs': None}
self.eud = None
self.ntcp_or_tcp = None
self.bin_count = max([len(dvh) for dvh in dvh_split])
self.dvh = np.zeros([self.bin_count, self.count])
# Get needed values not in DVHs table
for i in range(self.count):
# 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(dvh_split[i],
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))
self.dth = []
for i in range(self.count):
# Process dth_string to numpy array
try:
self.dth.append(
np.array(self.dth_string[i].split(','),
dtype='|S4').astype(np.float))
except Exception:
self.dth.append(np.array([0]))
# Store these now so they can be saved in DVH object without needing to query later
with DVH_SQL() as cnx:
self.physician_count = len(
cnx.get_unique_values(
'Plans', 'physician',
"study_instance_uid in ('%s')" % "','".join(self.uid)))
self.total_fxs = self.get_plan_values('fxs')
self.fx_dose = self.get_rx_values('fx_dose')
else:
self.count = 0