adict["latREM"].append(func.getLat(newU, 6))
# latSWS
if func.getLat(newU, 3) != "." and func.getLat(newU, 4) == ".":
adict["latSWS"].append(func.getLat(newU, 3))
elif func.getLat(newU, 3) == "." or func.getLat(newU, 4) == ".":
adict["latSWS"].append(".")
else:
# checking if 3 appears before 4
if func.getLat(newU, 3) <= func.getLat(newU, 4):
adict["latSWS"].append(func.getLat(newU, 3))
else:
adict["latSWS"].append(func.getLat(newU, 4))
p = func.getPS(newU) # index of onset of PS
if not p:
index = "."
adict["latPersistSLeep"].append(index)
else:
index = p[1]
if 0 in newU[:index]:
adict["latPersistSLeep"].append(".")
else:
adict["latPersistSLeep"].append(index / 2.0)
adict["S1"].append(func.getCount(newU)[0])
adict["S2"].append(func.getCount(newU)[1])
adict["S3"].append(func.getCount(newU)[2])
adict["S4"].append(func.getCount(newU)[3])
adict["Wake"].append(func.getCount(newU)[4])
def analyze(inputpath):
csv_files = glob.glob(inputpath + "*.csv")
# generate output folder
timestr = time.strftime("%Y%m%d-%H%M%S")
outputpath = inputpath + "output_" + timestr + "/"
if not os.path.exists(outputpath):
os.makedirs(outputpath)
# dictionary for the final output
adict = OrderedDict()
subject_group = []
output_header = [
"Subject", "SPn", "latS1", "latS2", "latREM", "latSWS",
"latPersistSLeep", "S1", "S2", "S3", "S4", "Wake", "REM", "Other",
"WAPSO", "FinalWake", "NWake_1", "NWake_2", "NWake_5", "Lout2Lon",
"LastSlp", "LastSlp_before_finalwake"
]
# initialize the output dictionary keys
for column_name in output_header:
adict[column_name] = []
for filename in csv_files:
# read from files
fname = os.path.basename(filename)
subject = fname[:fname.find('Slp')]
if subject not in subject_group:
subject_group.append(subject)
else:
# print "duplicate subject:"
# print filename
break
with open(filename, 'r') as f:
columns = defaultdict(list)
# read rows into a dictionary format
reader = csv.DictReader(
f, fieldnames=['subject', 'WPSP', 'labtime', 'sleepstate'])
try:
for row in reader: # read a row as {column1: value1, column2: value2,...}
for (k, v) in row.items(
): # go over each column name and value
columns[k].append(v)
except:
print("Reading error: " + filename)
raise
WPSP = columns['WPSP']
sleepstate = columns['sleepstate']
slp_list = []
slp_unit = []
# convert list of string to list of integers
WPSP = list(map(int, WPSP))
sleepstate = list(map(int, sleepstate))
ind8 = [i for i, x in enumerate(sleepstate) if x == 8]
ind9 = [i for i, x in enumerate(sleepstate) if x == 9]
for a, b in zip(ind8, ind9): #consider izip?
for i in range(a, b + 1):
slp_unit.append(Data(sleepstate[i],
i)) # appending sleep stages
slp_list.append(slp_unit) # slp_list: [Data1,Data2, Data3, ...]
slp_unit = []
slp_list2 = []
for unit in slp_list:
# spnlist = [-1, -1, -1, 1, 1,...]
spnlist = map(int,
columns['WPSP'][unit[0].pointer:unit[-1].pointer])
if any(spns > 0 for spns in spnlist):
slp_list2.append(unit)
# index of each first occured sleep state
# then calculate latency (/2.0)
for unit in slp_list2:
unit_start = 0
flag1 = 0 # if there is a change in unit
unit_end = -1
flag2 = 0 # if there is a change in unit
spn = int(columns['WPSP'][unit[0].pointer])
if spn < 0:
# replace lights out time with scheduled sleep offset
# find next positive Spn
indof8 = unit[unit_start].pointer
# print indof8
# print columns['WPSP'][unit[0].pointer]
while True:
flag1 = 1
indof8 += 1
unit_start += 1
if int(columns['WPSP'][indof8]) > 0:
# unit[0].resetData(int(columns['sleepstate'][indof8]),indof8)
break
# checking spn of 9
spn9 = int(columns['WPSP'][unit[-1].pointer])
if spn9 < 0:
# replace lights out time with scheduled sleep offset
# find next positive Spn
# print unit[0].pointer
indof9 = unit[unit_end].pointer
# print indof8
# print columns['WPSP'][unit[0].pointer]
while True:
flag2 = 1
indof9 -= 1
unit_end -= 1
if int(columns['WPSP'][indof9]) > 0:
# unit[-1].resetData(int(columns['sleepstate'][indof9]),indof9)
break
# making the Data.value into a new list
# newU is [8,,,,9] or [5,,,,,9]
if flag1 == 1 and flag2 == 1:
newU = func.getDataValue(unit[unit_start:unit_end + 1])
elif flag2 == 0:
newU = func.getDataValue(unit[unit_start:])
elif flag1 == 0:
newU = func.getDataValue(unit[:unit_end + 1])
else:
newU = func.getDataValue(unit)
# print newU
adict["Subject"].append(columns['subject'][unit[1].pointer])
# adict["SPn"].append(abs(int(columns['WPSP'][unit[0].pointer])))
# if int(columns['WPSP'][unit[1].pointer]) <0:
# print columns['subject'][unit[1].pointer], int(columns['WPSP'][unit[1].pointer])
adict["SPn"].append(abs(int(columns['WPSP'][unit[0].pointer])))
adict["latS1"].append(func.getLat(newU, 1))
adict["latS2"].append(func.getLat(newU, 2))
adict["latREM"].append(func.getLat(newU, 6))
# latSWS
if func.getLat(newU, 3) != "." and func.getLat(newU, 4) == ".":
adict["latSWS"].append(func.getLat(newU, 3))
elif func.getLat(newU, 3) == "." or func.getLat(newU, 4) == ".":
adict["latSWS"].append(".")
else:
# checking if 3 appears before 4
if func.getLat(newU, 3) <= func.getLat(newU, 4):
adict["latSWS"].append(func.getLat(newU, 3))
else:
adict["latSWS"].append(func.getLat(newU, 4))
p = func.getPS(newU) # index of onset of PS
if not p:
index = "."
adict["latPersistSLeep"].append(index)
else:
index = p[1]
if 0 in newU[:index]:
adict["latPersistSLeep"].append(".")
else:
adict["latPersistSLeep"].append(index / 2.0)
adict["S1"].append(func.getCount(newU)[0])
adict["S2"].append(func.getCount(newU)[1])
adict["S3"].append(func.getCount(newU)[2])
adict["S4"].append(func.getCount(newU)[3])
adict["Wake"].append(func.getCount(newU)[4])
adict["REM"].append(func.getCount(newU)[5])
adict["Other"].append(func.getCount(newU)[6])
adict["WAPSO"].append(func.countWake(newU, index))
fw = func.getFinalWake(newU)
if fw is None:
adict["FinalWake"].append(".")
else:
adict["FinalWake"].append(fw)
# get NWake: second parameter is wake time of 1, 2, or 5 minutes
adict["NWake_1"].append(func.getNWake(newU, 1))
adict["NWake_2"].append(func.getNWake(newU, 2))
adict["NWake_5"].append(func.getNWake(newU, 5))
adict["Lout2Lon"].append(func.getLout2Lon(newU))
# adding 2 more columns:
lastslp = func.SleepStageB49(newU)
if lastslp == None:
adict["LastSlp"].append(".")
else:
adict["LastSlp"].append(lastslp)
try:
lastslpfw = func.SleepStageB4FinalWake(newU)
except:
print("slp_stage_b4_finalwake error: " + filename)
print(spn)
raise
if lastslpfw == None:
adict["LastSlp_before_finalwake"].append(".")
else:
adict["LastSlp_before_finalwake"].append(lastslpfw)
# print filename # print filename after processing each file
## write to output
with open(outputpath + "output_unfilled.csv", "wb") as outfile:
writer = csv.writer(outfile)
writer.writerow(adict.keys())
export_data = zip_longest(*adict.values(), fillvalue="")
writer.writerows(export_data)
return outputpath