def OnGenerateReports(self, event):
"""
Download CSVs
:param event:
:return:
"""
downloaddirname = self.m_downloaddir.GetPath()
deltas = self.chDelta.GetValue()
if downloaddirname is not None and self.db is not None and self.proj is not None:
self.Destroy() # close window
xnat = XnatConnector(self.configfile, self.db)
xnat.connect()
subjects = xnat.getSubjectsDataframe(self.proj)
op = OPEXReport(subjects=subjects)
op.xnat = xnat
if op.generateCantabReport(projectcode=self.proj,
outputdir=downloaddirname,
deltas=True):
msg = "***CANTAB report Completed: %s" % downloaddirname
logging.info(msg)
else:
msg = "Error during CANTAB report"
logging.error(msg)
if op.generateBloodReport(projectcode=self.proj,
outputdir=downloaddirname):
msg = "***BLOOD report Completed: %s" % downloaddirname
logging.info(msg)
else:
msg = "Error during BLOOD report"
logging.error(msg)
dlg = wx.MessageDialog(self, msg, "Download CSVs", wx.OK)
dlg.ShowModal() # Show it
dlg.Destroy()
def __init__(self,
listofexperiments,
columns=None,
criteria=None,
**kwargs):
XnatConnector.__init__(self, **kwargs)
self.connect()
if listofexperiments is None:
listofexperiments = self.conn.inspect.datatypes('opex:')
xnatcompiler = {}
for experiment in listofexperiments:
print(('Compiling {}'.format(experiment)))
init = fetchData(connector=self,
experiment=experiment,
columns=columns,
criteria=criteria)
init.connector.conn.disconnect()
xnatcompiler[experiment] = {
'data': init.data,
'fields': init.fields,
'ID': init.IDS
}
self.compiler = xnatcompiler
dflist = [
self.compiler[key]['data'] for key in list(self.compiler.keys())
]
self.data = reduce(
lambda x, y: pd.merge(
x, y, on=['Subject', 'interval', 'Exercise', 'Gender']),
dflist)
def OnCSVDownload(self, event):
"""
Download CSVs
:param event:
:return:
"""
downloaddirname = self.m_downloaddir.GetPath()
deltas = self.chDelta.GetValue()
if downloaddirname is not None and self.db is not None and self.proj is not None:
xnat = XnatConnector(self.configfile, self.db)
xnat.connect()
subjects = xnat.getSubjectsDataframe(self.proj)
op = OPEXReport(subjects=subjects)
op.xnat = xnat
if op.downloadOPEXExpts(self.proj, downloaddirname, deltas):
msg = "***Downloads Completed: %s" % downloaddirname
logging.info(msg)
else:
msg = "Error during download"
logging.error(msg)
dlg = wx.MessageDialog(self, msg, "Download CSVs", wx.OK)
dlg.ShowModal() # Show it
dlg.Destroy()
def setUp(self):
configfile = join(expanduser('~'), '.xnat.cfg')
server = 'xnat-dev'
self.projectcode = 'TEST'
self.xnat = XnatConnector(configfile, server)
self.xnat.connect()
if not self.xnat.conn:
self.skipTest("Database not connecting")
class TestScanUploader(unittest.TestCase):
'''
Tests require a test XNAT instance to connect to with:
1. Login details in a file in the user home directory (.xnat.cfg)
2. Configuration name of the server to use for login
3. A project ID with subject as sampledata to test access
'''
def setUp(self):
"""
Requires MRI scans to upload to test XNAT instance
:return:
"""
scandir="D:\\Projects\\XNAT\\data\\S1\\scans\\3"
self.seriesnum = basename(scandir)
scanfiles = [f for f in listdir(scandir) if not isdir(join(scandir, f))]
if len(scanfiles) > 0:
self.dicomfile=join(scandir,scanfiles[0])
else:
self.skipTest('No DICOM test files found')
def tearDown(self):
print('Done')
def test_getScanType(self):
scanuploader = ScanUploader()
type = scanuploader.getScanType(scanuploader.default_scantype, self.dicomfile)
self.assertEqual(type, scanuploader.default_scantype, "Scan type not default")
def test_getModality(self):
scanuploader = ScanUploader()
type = scanuploader.getModality(self.dicomfile)
self.assertIsNotNone(type, 'Modality is none')
def test_getSeriesNumber(self):
scanuploader = ScanUploader()
type = scanuploader.getSeriesNumber(self.seriesnum,self.dicomfile)
self.assertIsNotNone(type, 'SeriesNumber is none')
self.assertEqual(int(type), int(self.seriesnum), 'Series number not matching')
def test_getSeriesDatestamp(self):
scanuploader = ScanUploader()
do = scanuploader.getSeriesDatestamp(self.dicomfile)
self.assertIsNotNone(do, 'Date is none')
self.assertIsInstance(do, datetime, 'Date is not datetime instance')
def testUpload(self):
'''
Will upload scan series - so don't run this often
:return:
'''
configfile = join(expanduser('~'), '.xnat.cfg')
server = 'xnat-dev'
self.xnat = XnatConnector(configfile, server)
self.xnat.connect()
if not self.xnat.conn:
self.skipTest("Database not connecting")
def rundownloads(database, projectcode, output):
xnat = XnatConnector(join(expanduser('~'), '.xnat.cfg'), database)
xnat.connect()
subjects = xnat.getSubjectsDataframe(projectcode)
op = OPEXReport(subjects=subjects)
op.xnat = xnat
outputdir = output
op.downloadOPEXExpts(projectcode=projectcode,
outputdir=outputdir,
deltas=True)
def testUpload(self):
'''
Will upload scan series - so don't run this often
:return:
'''
configfile = join(expanduser('~'), '.xnat.cfg')
server = 'xnat-dev'
self.xnat = XnatConnector(configfile, server)
self.xnat.connect()
if not self.xnat.conn:
self.skipTest("Database not connecting")
def OnGenerateReports(self, event):
"""
Download CSVs
:param event:
:return:
"""
downloaddirname = self.m_downloaddir.GetPath()
deltas = self.chDelta.GetValue()
if downloaddirname is not None and self.db is not None and self.proj is not None:
xnat = XnatConnector(self.configfile, self.db)
xnat.connect()
subjects = xnat.getSubjectsDataframe(self.proj)
if subjects is not None:
op = OPEXReport(subjects=subjects)
op.xnat = xnat
msg = "Generating CANTAB report ..."
logging.info(msg)
print(msg)
if op.generateCantabReport(projectcode=self.proj,
outputdir=downloaddirname,
deltas=deltas):
msg = "***CANTAB report Completed: %s" % downloaddirname
logging.info(msg)
else:
msg = "Error during CANTAB report"
logging.error(msg)
print(msg)
msg = "Generating BLOOD report ..."
logging.info(msg)
print(msg)
if op.generateBloodReport(projectcode=self.proj,
outputdir=downloaddirname,
deltas=deltas):
msg = "***BLOOD report Completed: %s" % downloaddirname
logging.info(msg)
else:
msg = "Error during BLOOD report"
logging.error(msg)
print(msg)
else:
msg = "Cannot list subjects from XNAT"
logging.error(msg)
print(msg)
# close connection
op.xnat.conn.disconnect()
def get_maxHR(subject):
home = expanduser("~")
configfile = join(home, '.xnat.cfg')
xnat = XnatConnector(configfile, 'opex')
xnat.connect()
criteria = [('xnat:subjectData/SUBJECT_ID', 'LIKE', '*'), 'AND']
columns = ['xnat:subjectData/SUBJECT_LABEL', 'opex:cosmed/INTERVAL', 'opex:cosmed/HR']
dsitype = 'opex:cosmed'
subj = xnat.conn.select(dsitype, columns).where(criteria)
xnat.conn.disconnect()
df = pd.DataFrame(list(subj)).\
set_index(['xnat_subjectdata_subject_label', 'interval']).\
loc[subject]
HR_max0, HR_max3 = float(df.loc['0']), float(df.loc['3'])
return HR_max0, HR_max3
class TestConnector(unittest.TestCase):
'''
Tests require a test XNAT instance to connect to with:
1. Login details in a file in the user home directory (.xnat.cfg)
2. Configuration name of the server to use for login
3. A project ID with subject as sampledata to test access
'''
def setUp(self):
configfile = join(expanduser('~'), '.xnat.cfg')
server = 'xnat-dev'
self.projectcode = 'TEST'
self.xnat = XnatConnector(configfile, server)
self.xnat.connect()
if not self.xnat.conn:
self.skipTest("Database not connecting")
def tearDown(self):
self.xnat.conn.disconnect()
def test_get_project(self):
projectcode = self.projectcode
proj = self.xnat.get_project(projectcode)
self.assertIsNotNone(proj, "Project not found")
self.assertEqual(projectcode, proj.id(), "Project code is not equal")
def test_get_projectPI(self):
projectcode = self.projectcode
proj = self.xnat.get_projectPI(projectcode)
lastname = 'Einstein'
self.assertIsNotNone(proj, "Project PI not found")
self.assertEqual(lastname, proj, "Project code is not equal")
def test_get_subjectbylabel(self):
projectcode = self.projectcode
subjectlabel = 'S0001'
subjectid = 'IRC5XNAT_S00001'
sid = self.xnat.get_subjectid_bylabel(projectcode, subjectlabel)
self.assertIsNotNone(sid, "Subject ID not found")
self.assertEqual(sid, subjectid, "Subject id is not equal")
def loadData(self):
output = "RefreshCounts_%s.csv" % datetime.today().strftime("%Y%m%d")
# output = "ExptCounts.csv"
# outputfile = join(self.cache, output)
# if exists(outputfile):
# report = OPEXReport(csvfile=outputfile)
# logging.info("Loading via cache")
# else:
# logging.info("Loading from database")
configfile = self.dbconfig
xnat = XnatConnector(configfile, self.database)
try:
xnat.connect()
if xnat.testconnection():
print("...Connected")
output = "ExptCounts.csv"
# outputfile = join(self.cache, output)
# if access(outputfile, R_OK):
# csv = outputfile
# else:
# csv = None
subjects = xnat.getSubjectsDataframe(self.project)
msg = "Loaded %d subjects from %s : %s" % (
len(subjects), self.database, self.project)
logging.info(msg)
report = OPEXReport(subjects=subjects)
report.xnat = xnat
# Generate dataframes for display
self.df_participants = report.getParticipants()
logging.info('Participants loaded')
#print self.df_participants
self.df_report = report.printMissingExpts(self.project)
self.df_report.sort_values(by=['MONTH', 'Subject'],
inplace=True,
ascending=False)
logging.info("Missing experiments loaded")
#print self.df_report.head()
# Get expts
self.df_expts = report.getExptCollection(
projectcode=self.project)
logging.info("Experiment collection loaded")
#print self.df_expts.head()
except IOError:
logging.error("Connection error - terminating app")
print("Connection error - terminating app")
sys.exit(1)
finally:
xnat.conn.disconnect()
def OnTest(self, e):
"""
Test connection is correctly configured
:param e:
:return:
"""
self.tcResults.Clear()
(db, proj) = self.__loadConnection()
xnat = XnatConnector(self.configfile, db)
xnat.connect()
msg = "Connection to %s for project=%s\n" % (db, proj)
self.tcResults.AppendText(msg)
if xnat.testconnection():
msg = "CONNECTION SUCCESSFUL"
if xnat.get_project(proj).exists():
msg += " and Project exists"
else:
msg += " but Project DOES NOT exist"
else:
msg = "CONNECTION FAILED - please check config"
self.tcResults.AppendText(msg)
def __init__(self, pathtofile, expt, *args):
XnatConnector.super(*args)
self.pathtofile = pathtofile
'--config',
action='store',
help='database configuration file (overrides ~/.xnat.cfg)')
parser.add_argument('--filepath',
action='store',
help='Path to file containing expts to remove',
default="Q:\\DATA\\expts_removed.xlsx")
parser.add_argument('--expt',
action='store',
help='Expt (sheet) containing expts to remove',
default="0")
args = parser.parse_args()
pathtofile = args.filepath
xnat = XnatConnector(configfile, args.database)
xnat.connect()
print('Welcome to Xnat deleter: any shitty text-based adventure \n')
print('It seems you have shitty data that you wish to remove')
single = input('Removing (s)ingle or (b)atch of expts?')
if single == 's':
print(
'So you wish to only remove one experiment? Put in your expt ID tag now'
)
expttag = input('Experiment ID: ')
time.sleep(1)
print(
'\nNow before going ahead, are you sure you are not high on drugs?'
)
def __init__(self, rootdir, xsd, *args):
XnatConnector.super(*args)
self.connect()
self.rootdir = rootdir