def study_CheckSubjects(subid):
SubjectSummary = []
conn_qc = studydata.db_connection
#for i in range(0,5,1):
#S=study.subjectlist[i]
#for S in study.subjectlist:
if subid in study.quarantine.subjects:
S = study.quarantine.subjects[subid]
D = CheckSubject.CheckSubject(S)
#D.InitializeScansCogRes()
D.InitializeScansRANN()
print "\n-----------------------------"
print "============================="
print "========= %s =========" % (D.Subject.subid)
print "======= %s =======" % ("Acquistion Problems")
for V in D.Subject.visitlist:
Files = os.listdir(V.path)
D.InspectImages(Files, V.path)
SubjectSummary.append(D)
print "======= %s =======" % ("Found Scans")
D.CheckAllScansCollected()
print "======= %s =======" % ("Missing Scans")
D.CheckAllScansNOTCollected()
print "======= %s =======" % ("QC Assessment")
D.PrintQCAssessment(conn_qc, study.name)
else:
print "Subject: %s not imported" % (subid)
def study_Check_One_Excluded(subid, study, studydata):
# Check the acquisition parameters and
# for missing data from one participant
# expected to be in quarantine
SubjectsSummary = []
conn_qc = studydata.db_connection
D = []
if subid in study.excluded.subjects:
S = study.excluded.subjects[subid]
D = CheckSubject.CheckSubject(S)
study_CheckSubject(D, study, studydata, conn_qc)
else:
print "Subject: %s not imported" % (subid)
return D
def study_Check_One_Subjects(subid, study, studydata):
# Check the acquisition parameters and
# for missing data from one participant
# expected to be in quarantine
SubjectsSummary = []
conn_qc = studydata.db_connection
D = []
# Check this one subject
if subid in study.subjects:
# extract the subject structure
S = study.subjects[subid]
# initialize a scan structure for this subject
D = CheckSubject.CheckSubject(S)
# fill in the structure based on what was found
# but this step collapses across visits
study_CheckSubject(D, study, studydata, conn_qc)
else:
print "Subject: %s not imported" % (subid)
return D
def check_RANN_Subject_Behav(subid, studydata, study):
D = CheckSubject.CheckSubject(subid)
# python does not use switch/case statements
D.InitializeScansRANN()
RANNBehav = {}
# Tasks = ['DgtSym','LetComp','PaperFold','LetSet','Syn','Ant','LogMem','MatReas','PairAssoc','PattComp','WordOrder']
Measures = ['PropOnTimeCor', 'medianAllRT']
conn_qc = studydata.db_connection
for index in D.TaskList:
task = D.Scans[index]['SeriesName'][0:-3]
#print task
RANNBehav[task] = {}
sqlcommand = "SELECT subid"
for meas in Measures:
sqlcommand = sqlcommand + ", %s_%s" % (task, meas)
sqlcommand = sqlcommand + " FROM cnsdivdb.RANNBehav where subid='%s'" % (
subid)
#print sqlcommand
try:
conn_qc.cur.execute(sqlcommand)
for row_dict in conn_qc.cur.fetchall():
for meas in Measures:
if row_dict[task + "_" + meas] > -1:
RANNBehav[task][meas] = row_dict[task + "_" + meas]
except:
for meas in Measures:
RANNBehav[task][meas] = -9999
print subid
for task in RANNBehav.iteritems():
Str = "%15s:" % (task[0])
for meas in Measures:
if len(task[1]) > 0:
Str = "%s %s=%3.4f," % (Str, meas, task[1][meas])
else:
Str = "%s no data found" % (Str)
if len(task[1]) > 0:
if task[1][Measures[0]] < 0.5:
Str = "%s <<<<<< " % (Str)
print Str
def study_Check_All_Subjects(study, studydata):
# Check the acquisition paramet# check subjects folderers and
# for missing data from all participants
# in the Subjects folder
SubjectsSummary = []
conn_qc = studydata.db_connection
for S in study.subjectlist:
D = CheckSubject.CheckSubject(S)
#D.InitializeScansCogRes()
# python does not use switch/case statements
if study.name is "RANN":
D.InitializeScansRANN()
elif study.name is "CogRes":
D.InitializeScansCogRes()
elif study.name is "iLS":
D.InitializeScansILS()
elif study.name is "WHICAP":
D.InitializeScansWHICAPV3()
elif study.name is "AZ2":
D.InitializeScansAZ2()
elif study.name is "Exercise58":
D.InitializeScansEx58()
else:
break
print "\n-----------------------------"
print "============================="
print "========= %s =========" % (D.Subject.subid)
print "======= %s =======" % ("Acquistion Problems")
for V in D.Subject.visitlist:
Files = os.listdir(V.path)
D.InspectImages(Files, V.path)
print "======= %s =======" % ("Found Scans")
D.CheckAllScansCollected()
print "======= %s =======" % ("Missing Scans")
D.CheckAllScansNOTCollected()
print "======= %s =======" % ("QC Assessment")
D.PrintQCAssessment(conn_qc, study.name)
SubjectsSummary.append(D)
return SubjectsSummary
'''
import os
import sys
import CheckSubject
%run study.py
reload(CheckSubject)
conn_main = studydata.db_connection_main
conn_qc = studydata.db_connection
SubjectSummary = []
for S in study.subjectlist:
#for i in range(0,5,1):
#S=study.subjectlist[i]
#for S in study.subjectlist:
D=CheckSubject.CheckSubject(S)
#D.InitializeScansCogRes()
D.InitializeScansILS()
#D.InitializeScansRANN()
print "\n-----------------------------"
print "============================="
print "========= %s ========="%(D.Subject.subid)
print "======= %s ======="%("Acquistion Problems")
for V in D.Subject.visitlist:
Files=os.listdir(V.path)
D.InspectImages(Files,V.path)
SubjectSummary.append(D)
print "======= %s ======="%("Missing Scans")
D.CheckAllScansCollected()
print "======= %s ======="%("QC Assessment")
D.PrintQCAssessment(conn_qc,study.name)
def check_CogRes_Subject_Behav(subid, studydata, study):
# Do this to initialize the list of scans
D = CheckSubject.CheckSubject(subid)
D.InitializeScansCogRes()
conn_qc = studydata.db_connection
# create list of measures to look at
ECFMeasure = 'DualNonComp_NCor'
LSMeasure = 'NumCor_6r'
# create the column names for the output spreadsheet
ColumnNames = []
# since ECF behavioral data is collapsed across runs only one value is
# extracted from the dB
ECFFlag = True
# cycle over the series in the Scan list and make sure to only check
# the ECF behavior once
for index in D.TaskList:
if ECFFlag and D.Scans[index]['SeriesName'].find('ECF') > -1:
ECFFlag = False
ColumnNames.append("%s_%s" % ('ECF', ECFMeasure))
elif D.Scans[index]['SeriesName'].find('LS') > -1:
LSRun = D.Scans[index]['SeriesName'][-1]
ColumnNames.append(
"%s_%s%s" %
(D.Scans[index]['SeriesName'][0:-3], LSMeasure, LSRun))
one_list = []
for index in range(0, len(ColumnNames), 1):
task = ColumnNames[index]
sqlcommand = "SELECT subid"
sqlcommand = "%s,%s" % (sqlcommand, task)
if task.find('ECF') > -1:
sqlcommand = sqlcommand + " FROM cnsdivdb.ECFBehav where subid='%s'" % (
subid)
elif task.find('LS') > -1:
sqlcommand = sqlcommand + " FROM cnsdivdb.LSBehav where subid='%s'" % (
subid)
else:
pass
# print sqlcommand
try:
# ret is the number of rows returned
ret = conn_qc.cur.execute(sqlcommand)
if ret is 0:
one_list.append(-9999)
elif ret is 1:
row_dict = conn_qc.cur.fetchall()
value = row_dict[0][ColumnNames[index]]
if value > 0:
one_list.append(1)
else:
one_list.append(0)
elif ret > 1:
MultipleRowFlag = True
for row_dict in conn_qc.cur.fetchall():
# value from first row
if MultipleRowFlag:
value = row_dict[ColumnNames[index]]
if value > 0:
one_list.append(1)
MultipleRowFlag = False
if MultipleRowFlag:
# if this flag is still true then there are multiple
# rows in the dB with no data in them
one_list.append(-9999)
except:
one_list.append(-9999)
print "Behavioral Summary: %s" % (subid)
for i in range(0, len(ColumnNames), 1):
print "%s\t%d" % (ColumnNames[i], one_list[i])