def setUpClass(cls):
# Set up a database connection
cls.db = Database.from_key('tests/credentials',
'config/credentials.key')
# Select a patient
query = 'SELECT TOP(1) ID, patientID FROM patientRepresentations'
res0 = cls.db.run(query)
cls.patientRepID = res0.rows[0].ID
def roi_query_helper(prepID):
'''
Get all ROI's for a patient ID
'''
query = '''
SELECT TOP(2) patientRepID, ID, name
FROM RegionsOfInterest
WHERE patientRepID = {}
ORDER BY name asc
'''.format(prepID)
return cls.db.run(query).rows
# Store patientRepID and a few ROI names and IDs
res1 = roi_query_helper(cls.patientRepID)
# Get a few masks
res2, _ = cls.db.regions_of_interest.get_masks(
cls.patientRepID, [str(r.name) for r in res1])
cls.masks = list(res2.values())
def setUpClass(cls):
# Set up a database connection
cls.db = Database.from_key('tests/credentials',
'config/credentials.key')
# Select a patient
query = 'SELECT TOP(1) ID, patientID FROM patientRepresentations'
res = cls.db.run(query)
cls.patientRepID = res.rows[0].ID
# Get a dose grid for a patient
res0 = cls.db.radiotherapy_sessions.get_session_ids(cls.patientRepID)
cls.dg = cls.db.radiotherapy_sessions.get_dose_grid(res0.rows[0][0])
def roi_query_helper(prepID):
'''
Get all ROI's for a patient ID
'''
query = '''
SELECT TOP(1) patientRepID, ID, name
FROM RegionsOfInterest
WHERE patientRepID = {}
ORDER BY name asc
'''.format(prepID)
return cls.db.run(query).rows[0]
# Store patientRepID and name of ROIs with a certain number of occurrences
res1 = roi_query_helper(cls.patientRepID)
res2 = cls.db.regions_of_interest.get_id_by_patient_rep_id_name(
res1.patientRepID, str(res1.name))
cls.mask = cls.db.regions_of_interest.get_mask(res2)
# Create a dose mask
cls.dm = DoseMask(cls.mask, cls.dg)
def setUpClass(cls):
# Set up a database connection
cls.db = Database.from_key('tests/credentials',
'config/credentials.key')
# Select a patient
query = 'SELECT TOP(1) ID, patientID FROM patientRepresentations'
res = cls.db.run(query)
cls.patientRepID = res.rows[0].ID
cls.patientID = res.rows[0].patientID
def roi_query_helper(count):
'''
Get a patientRepID and ROI name that appears a certain number of times
'''
query = '''
WITH query1 as (
SELECT patientRepID, name, count(*) as count
FROM RegionsOfInterest
GROUP BY name, patientRepID
)
SELECT TOP(1) * FROM query1 WHERE count = {}
'''.format(count)
res = cls.db.run(query)
return res.rows[0]
# Store patientRepID and name of ROIs with a certain number of occurrences
res0 = roi_query_helper(1)
cls.one_roi = [res0.patientRepID, str(res0.name)]
res1 = roi_query_helper(2)
cls.many_rois = [res1.patientRepID, str(res1.name)]
def setUpClass(cls):
# Set up a database connection
cls.db = Database.from_key('tests/credentials',
'config/credentials.key')
query = 'SELECT TOP(1) patientID FROM Patients'
res = cls.db.run(query)
cls.patientID = res.rows[0].patientID
def setUpClass(cls):
# Set up a database connection
cls.db = Database.from_key('tests/credentials',
'config/credentials.key')
cls.rois = ['l_parotid', 'r_parotid']
prepIDs = cls.db.regions_of_interest.get_patient_rep_ids_with_rois(
cls.rois)
if len(prepIDs) >= 2:
cls.patientRep_1 = prepIDs[0]
cls.patientRep_2 = prepIDs[1]
def setUpClass(cls):
# Set up a database connection
cls.db = Database.from_key('tests/credentials',
'config/credentials.key')
# Select a patient
query = 'SELECT TOP(1) ID, patientID FROM patientRepresentations'
res = cls.db.run(query)
cls.patientRepID = res.rows[0].ID
cls.patientID = res.rows[0].patientID
# Files to delete
cls.file_path = 'tests/files/'
cls.to_remove = []
def setUpClass(cls):
# Set up a database connection
cls.db = Database.from_key('tests/credentials',
'config/credentials.key')
# Select a patient
query = 'SELECT TOP(1) ID, patientID FROM patientRepresentations'
res = cls.db.run(query)
cls.patientRepID = res.rows[0].ID
cls.patientID = res.rows[0].patientID
res = cls.db.radiotherapy_sessions.get_session_ids(cls.patientRepID)
# Normal dose grid
cls.dg = cls.db.radiotherapy_sessions.get_dose_grid(res.rows[0][0])
# Scaled dose grid
cls.dg_scaled = cls.db.radiotherapy_sessions.get_dose_grid(
res.rows[0][0])
cls.dg_scaled.dose_scaling_factor = 0.5
def setUpClass(cls):
# Set up a database connection
cls.db = Database.from_key('tests/credentials',
'config/credentials.key')
# Select a patient
query = 'SELECT TOP(1) ID, patientID FROM patientRepresentations'
res = cls.db.run(query)
cls.patientRepID = res.rows[0].ID
def roi_query_helper(prepID):
'''
Get all ROI's for a patient ID
'''
query = '''
SELECT TOP(1) patientRepID, ID, name
FROM RegionsOfInterest
WHERE patientRepID = {}
ORDER BY name asc
'''.format(prepID)
return cls.db.run(query).rows[0]
# Store patientRepID and name of ROIs with a certain number of occurrences
res1 = roi_query_helper(cls.patientRepID)
res2 = cls.db.regions_of_interest.get_id_by_patient_rep_id_name(
res1.patientRepID, str(res1.name))
base_mask = cls.db.regions_of_interest.get_mask(res2)
# Make one mask that is contiguous
cont_pts = [[i, j, k] for i in range(10) for j in range(10)
for k in range(10)]
cls.good_mask = tf.general.fill_mask(base_mask, cont_pts)
# And create one that is discontiguous
discont_pts = [[i, j, k] for i in range(10) for j in range(10)
for k in range(10) if k < 4 or k > 5]
cls.bad_mask = tf.general.fill_mask(base_mask, discont_pts)
'-q': 0,
'-d': 1,
'-v': 2
}
return verb_dict[verbosity_flags[0]]
# RUN ALL UNIT TESTS ==============================================================================
if __name__ == '__main__':
db = 'OncospaceHeadNeck'
us = 'oncoguest'
pw = '0ncosp@ceGuest'
#connect to database
dbase = Database(None, None, db, us, pw) #how to close?
#initialize query classes
PRQ = PatientRepresentationsQueries(dbase)
ROIQ = RegionsOfInterestQueries(dbase)
AQ = AssessmentsQueries(dbase)
RSQ = RadiotherapySessionsQueries(dbase)
manager = Manager()
#create patient list
patients = PRQ.get_patient_id_LUT()
masks = ROIQ.get_roi_names()
module = 'dose'
output = []
#output = np.tile(-1, (10, len(masks)))#(len(patients), len(masks)))
i = 0
def __init__(self, dr=None, ho=None, db='OncospaceHeadNeck', us='oncoguest', pw='0ncosp@ceGuest'):
#connect to database
self.dbase = Database(dr, ho, db, us, pw)
self.manager = Manager()
# ### Import modules # In[1]: from __future__ import print_function from oncotools.connect import Database from oncotools.data_elements.dose_map import DoseMask import numpy as np # ### Connect to the database # In[2]: db = Database(db='OncospaceHeadNeck', us='oncoguest', pw='0ncosp@ceGuest') # ### Patient ID and Patient representation ID # # Individual patients are identified by a patientID. # # Each patient has at least one patient representations. A patient representation corresponds to one scan (a certain geometry) and a set of structures from that one scan. # In[3]: # Map patient representation ID to patient ID patLUT = db.patient_representations.get_patient_id_LUT() # Map patient ID to patient representation ID(s) prepLUT = db.patient_representations.get_patient_rep_id_LUT()