class TestDBquery(unittest2.TestCase):
def setUp(self):
self.dbi = DBI()
self.dbi.connect()
# try:
# self.deleteData()
# except OperationalError as e:
# print(e.args[0])
# self.tearDown()
def deleteData(self):
# Reset all data so tests will work - so only use with a test db
self.dbi.deleteData('seriesprocess')
self.dbi.deleteData('dicomfiles')
self.dbi.deleteData('dicomdata')
def tearDown(self):
self.dbi.conn.close()
def test_getCaptions(self):
data = self.dbi.getCaptions()
expected = 0
print('Captions: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getRefs(self):
data = self.dbi.getRefs()
expected = 0
print('Refs: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getDescription(self):
caption = 'QSM'
data = self.dbi.getDescription(caption)
expected = 0
print('Description: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getCaption(self):
caption = 'qsm'
data = self.dbi.getCaption(caption)
expected = 0
print('Caption: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getProcessModule(self):
caption = 'qsm'
data = self.dbi.getProcessModule(caption)
expected = 0
print('Module: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getProcessClass(self):
caption = 'qsm'
data = self.dbi.getProcessClass(caption)
expected = 0
print('Class: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getFiles(self):
uuid = '5d74a20b44ec1dfd0af4fbc6bb680e0f557c14a08a143b843ef40977697e2bea'
data = self.dbi.getFiles(uuid)
expected = 0
print('Files: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getNoFiles(self):
uuid = 't10001'
data = self.dbi.getFiles(uuid)
expected = 0
print('Files: ', data)
self.assertEqual(expected, len(data))
def test_addDicomdata(self):
dicomdata = {
'uuid': 't10000',
'patientid': 'p1',
'patientname': 'test patient',
'seriesnum': '1.001.111',
'sequence': 'ftest',
'protocol': 'aaa',
'imagetype': 'M'
}
try:
rtn = self.dbi.addDicomdata(dicomdata)
self.assertEqual(rtn, 1, 'Dicom data add failed')
except IntegrityError as e:
self.skipTest(e.args[0])
def test_hasUuid(self):
uuid = 't10000'
self.assertIs(self.dbi.hasUuid(uuid), True, 'Data already added')
def test_addDicomdataExisting(self):
dicomdata = {
'uuid': 't10000',
'patientid': 'p1',
'patientname': 'test patient',
'seriesnum': '1.001.111',
'sequence': 'ftest',
'protocol': 'aaa',
'imagetype': 'M'
}
try:
self.assertRaises(IntegrityError, self.dbi.addDicomdata, dicomdata)
except AssertionError as e:
self.skipTest(e.args[0])
def test_addDicomfileExisting(self):
uuid = 't10000'
dicomfile = "D:\\Projects\\XNAT\\data\\S1\\scans\\3\\1001DS.MR.RESEARCH_16022_OPTIMIZING_EXERCISE.0003.0001.2017.02.24.15.41.05.593750.93525560.IMA"
try:
self.assertRaises(IntegrityError, self.dbi.addDicomfile, uuid,
dicomfile)
#self.assertEqual(rtn, 1, 'Dicom file add failed')
except AssertionError as e:
self.skipTest(e.args[0])
def test_addDicomfile(self):
uuid = 't10000'
dicomfile = "D:\\Projects\\XNAT\\data\\S1\\scans\\3\\1001DS.MR.RESEARCH_16022_OPTIMIZING_EXERCISE.0003.0001.2017.02.24.15.41.05.593750.93525560.IMA"
try:
rtn = self.dbi.addDicomfile(uuid, dicomfile)
self.assertEqual(rtn, 1, 'Dicom file add failed')
except IntegrityError as e:
self.skipTest(e.args[0])
def test_getUuids(self):
data = self.dbi.getUuids()
expected = 0
print('UUIDS: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getNumberFiles(self):
uuid = '5d74a20b44ec1dfd0af4fbc6bb680e0f557c14a08a143b843ef40977697e2bea'
data = self.dbi.getNumberFiles(uuid)
expected = 0
print('Num files: ', data)
self.assertIsNotNone(data)
self.assertGreater(data, expected)
def test_getDicomdataAll(self):
uuid = 't10000'
field = 'all'
data = self.dbi.getDicomdata(uuid, field)
expected = 0
print('Dicomdata for: ', field, '=', data)
self.assertIsNotNone(data)
self.assertGreater(data, expected)
def test_getDicomdata(self):
uuid = 't10000'
field = 'protocol'
data = self.dbi.getDicomdata(uuid, field)
expected = 0
print('Dicomdata for: ', field, '=', data)
self.assertIsNotNone(data)
self.assertGreater(data, expected)
def test_getRef(self):
pname = 'QSM'
expected = 'qsm'
data = self.dbi.getRef(pname)
self.assertEqual(expected, data)
# INSERTING DATA - USE TEST DB ONLY
# def test_setSeriesProcess(self):
# uuid = '5d74a20b44ec1dfd0af4fbc6bb680e0f557c14a08a143b843ef40977697e2bea'
# pid = 1
# server = 'AWS'
# status = 1
# starttime = datetime.datetime.now()
# try:
# rtn = self.dbi.setSeriesProcess(uuid, pid,server,status,starttime)
# self.assertEqual(rtn, 1, 'Series Process add failed')
# except IntegrityError as e:
# self.skipTest(e.args[0])
def test_getActiveProcesses(self):
data = self.dbi.getActiveProcesses()
print(data)
def test_deleteSeriesData(self):
uuid = '5d74a20b44ec1dfd0af4fbc6bb680e0f557c14a08a143b843ef40977697e2bea'
self.dbi.deleteSeriesData(uuid)
class DicomThread(threading.Thread):
def __init__(self, wxObject, filelist):
threading.Thread.__init__(self)
self.wxObject = wxObject
self.filelist = filelist
self.db = DBI()
def run(self):
print('Starting DICOM thread run')
n = 1
try:
event.set()
lock.acquire(True)
for filename in self.filelist:
try:
if not self.db.hasFile(filename):
dcm = pydicom.read_file(filename)
updatemsg = "Detecting DICOM data ... %d of %d" % (
n, len(self.filelist))
wx.PostEvent(self.wxObject, DataEvent((updatemsg, [])))
# self.m_status.SetLabelText(updatemsg)
n += 1
# Check DICOM header info
series_num = str(dcm.SeriesInstanceUID)
uuid = generateuid(series_num)
imagetype = str(dcm.ImageType[2])
dicomdata = {
'uuid': uuid,
'patientid': str(dcm.PatientID),
'patientname': str(dcm.PatientName),
'seriesnum': series_num,
'sequence': str(dcm.SequenceName),
'protocol': str(dcm.ProtocolName),
'imagetype': imagetype
}
if not self.db.hasUuid(uuid):
self.db.addDicomdata(dicomdata)
if not self.db.hasFile(filename):
self.db.addDicomfile(uuid, filename)
except InvalidDicomError:
logging.warning("Not valid DICOM - skipping: ", filename)
continue
############## Load Series Info
for suid in self.db.getUuids():
numfiles = self.db.getNumberFiles(suid)
item = [
True,
self.db.getDicomdata(suid, 'patientname'),
self.db.getDicomdata(suid, 'sequence'),
self.db.getDicomdata(suid, 'protocol'),
self.db.getDicomdata(suid, 'imagetype'),
str(numfiles),
self.db.getDicomdata(suid, 'seriesnum')
]
wx.PostEvent(self.wxObject, DataEvent((suid, item)))
except Exception as e:
msg = 'ERROR encountered during DICOM thread: %s' % e.args[0]
finally:
n = len(self.db.getNewUuids())
if n > 0:
msg = "Total Series loaded: %d" % n
logger.info(msg)
elif len(self.db.getUuids()) > 0:
msg = "Series already processed. Remove via Status Panel to repeat upload."
logger.info(msg)
else:
logging.error(msg)
if self.db.conn is not None:
self.db.closeconn()
wx.PostEvent(self.wxObject, DataEvent((msg, [])))
# self.terminate()
lock.release()
event.clear()