def test_surfstar_Multiplexer():
""" Test SURF* on 6-bit Multiplexer """
#New parameters
options['algorithm'] = 'surfstar'
Scores = S.runSURF(header, x, y, attr, var, distArray, options)
print("SURF* + 6-bit Multiplexer ")
print(str(Scores))
#Check that score list is not empty
assert Scores != None
#Check that a score for all features is output
assert len(Scores) == 6 #6-bit Multiplexer problem
#Check that all scores fall between -1 and 1
assert max(Scores) <= 1 and min(Scores) >= -1
#Check that the address bits (indexed as features 0 and 1) have the top scores as expected.
indexTopScore = Scores.index(max(Scores))
assert indexTopScore == 0 or indexTopScore == 1
Scores.pop(indexTopScore)
indexTopScore = Scores.index(max(Scores))
assert indexTopScore == 0
def test_surfstar_GWAS_Sim():
""" Test SURF* on GWAS_Sim Missing Data"""
#New parameters
options['algorithm'] = 'surfstar'
Scores = S.runSURF(header, x, y, attr, var, distArray, options)
print("SURF* + GWAS_Sim MD ")
print(str(Scores))
#Check that score list is not empty
assert Scores != None
#Check that a score for all features is output
assert len(Scores) == 20 #GWAS simulated dataset
#Check that all scores fall between -1 and 1
assert max(Scores) <= 1 and min(Scores) >= -1
#Check that the address bits (indexed as features 0 and 1) have the top scores as expected.
indexTopScore = Scores.index(max(Scores))
assert indexTopScore == 18 or indexTopScore == 19
Scores.pop(indexTopScore)
indexTopScore = Scores.index(max(Scores))
assert indexTopScore == 18
import multisurf as MS
print('Running MultiSURF or MultiSURF* + TuRF')
fun = MS.runMultiSURF
Scores,x,var,lost,table = T.runTurf(header,x,y,attr,var,distArray,pct,iterations,fun,options,cmn)
options['algorithm'] = algorithm + "-turf"
elif(algorithm == 'relieff'):
import relieff as R
print('Running Relieff')
Scores = R.runReliefF(header,x,y,attr,var,distArray,options)
elif(algorithm == 'surf' or algorithm =='surfstar'):
import surf as S
print('Running SURF or SURF*')
Scores = S.runSURF(header, x, y, attr, var, distArray, options)
elif(algorithm == 'multisurf' or algorithm == 'multisurfstar'):
if(var['classType'] == 'multiclass'):
import multisurf as MS
print('Running MultiSURF or MultiSURF*')
Scores = MS.runMultiSURF(header, x, y, attr, var, distArray, options)
#-----------------------------------------------------------------------------#
# create new data files of some number of top scored attributes
ordered_attr = io.createScoresFile(header, var, Scores, options,
prog_start, turfpct, table, lost)
if(options['topattr'] > 0):
io.create_subset(header, x, y, options, ordered_attr)
if(options['testdata'] != None):
io.create_test_subset(tdata, options, ordered_attr)
options['algorithm'] = algorithm + "-turf"
elif (algorithm == 'relieff'):
import relieff as R
Scores = R.runReliefF(header, x, y, attr, var, distArray, options)
elif (algorithm == 'multisurf'):
if (var['classType'] == 'multiclass'):
import mcms as MS
else:
import multisurf as MS
Scores = MS.runMultiSURF(header, x, y, attr, var, distArray, options)
elif (algorithm == 'surf' or algorithm == 'surfstar'):
import surf as S
Scores = S.runSURF(header, x, y, attr, var, distArray, options)
#-----------------------------------------------------------------------------#
# create new data files of some number of top scored attributes
ordered_attr = io.createScoresFile(header, var, Scores, options, prog_start,
turfpct, table, lost)
if (options['topattr'] > 0):
io.create_subset(header, x, y, options, ordered_attr)
if (options['testdata'] != None):
io.create_test_subset(tdata, options, ordered_attr)
if (V):
ctime = "[" + tm.strftime("%H:%M:%S") + "]"
print(ctime + " Overall program time(sec) = " +
str(tm.time() - prog_start))
###############################################################################