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Copy pathsingle_patient_parser.py
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175 lines (161 loc) · 7.6 KB
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import csv
class SinglePatientData():
def __init__(self, file_path, patient_id, bsz, process_id):
self.file_path = file_path
self.process_id = process_id
self.bsz = bsz
with open(file_path) as pat_01: csv_1_list = list(csv.reader(pat_01, delimiter=","))
self.lst = csv_1_list
self.labelsDict = {
1 : [1,1,1,1,1,1,1,1],
2 : [0,0,0,0],
3 : [0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0],
4 : [0,0,0,0],
5 : [1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1],
6 : [1,1,1,0,0,1,0,1],
7 : [0,0,0,0,0,0],
9 : [0,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],
10 : [0,1,1,1,1,1,0,1,1,1,1,1,1,0,0,1,0,1,0,1,0,0],
11 : [1,1,1,0,1,1],
12 : [0,0,0,0],
13 : [0,0,0,0,0,0,0,0,0,0,0],
14 : [0,0,1,0,0,1,0,1,0,0,0,0,0],
15 : [1,1,1,1,1,1,1,0,1,1],
16 : [0,0,1,1,1,1,1,1,1,1,1,1,1,1],
20 : [1,1,1,1,1,1]
}
self.onLeftDict = {1: False, 2: False, 3: False, 4: False, 5: True, 6: False, 7: False, 9:False, 10:False, 11:True, 12 : False, 13:False, 14:False, 15: True, 16:False, 20:False}
self.batches, self.labels = self.create_batches_and_labels(self.bsz, csv_1_list, self.labelsDict[patient_id], patient_id)
def place_paretic_side_first(self, days_list, patient_id):
if self.onLeftDict[patient_id]:
return days_list
else:
for i in range(len(days_list)):
for j in range(len(days_list[i])):
left_measures = days_list[i][j][2:9]
right_measures = days_list[i][j][11:]
days_list[i][j] = days_list[i][j][:2] + right_measures + days_list[i][j][9:11] + left_measures
return days_list
def split_by_day(self, csv_file, patient_id):
csv_file.pop(0)
single_day_list, days_list, current_date = [], [], csv_file[0][0]
for entry in csv_file:
if entry[0] == current_date:
single_day_list.append(entry)
else:
current_date = entry[0]
days_list.append(single_day_list)
single_day_list = [entry]
return self.place_paretic_side_first(days_list, patient_id)
def create_batches_and_labels(self, bsz, csv_file, labels_list, patient_id):
batches, labels = [], []
days_list = self.split_by_day(csv_file, patient_id)
for i in range(len(days_list)):
if i == 0:
c = 1
if len(days_list) == len(labels_list):
lst = days_list[i]
label = labels_list[i]
# line incompatible with python 2 and earlier
day_split_batches = [lst[j:j + bsz] for j in range(0, len(lst), bsz)]
day_split_labels = [label] * len(day_split_batches)
batches, labels = batches + day_split_batches, labels + day_split_labels
return batches, labels
def get_next_batch(self):
bch = self.batches.pop()
l = self.labels.pop()
lbl = [l] * len(bch)
return self.process(self.process_id, bch, lbl)
def process(self, process_id, batch, lbl):
processed_reads = []
processed_labels = []
if process_id == 1:
for read in batch:
try:
paretic_pos1 = float(read[2])
paretic_pos2 = float(read[3])
paretic_pos3 = float(read[4])
paretic_pos4 = float(read[5])
paretic_pos5 = float(read[6])
paretic_pos6 = float(read[7])
paretic_pos7 = float(read[8])
non_paretic_pos1 = float(read[11])
non_paretic_pos2 = float(read[12])
non_paretic_pos3 = float(read[13])
non_paretic_pos4 = float(read[14])
non_paretic_pos5 = float(read[15])
non_paretic_pos6 = float(read[16])
non_paretic_pos7 = float(read[17])
t = [paretic_pos1 - non_paretic_pos1, paretic_pos2 - non_paretic_pos2,
paretic_pos3 - non_paretic_pos3, paretic_pos4 - non_paretic_pos4,
paretic_pos5 - non_paretic_pos5, paretic_pos6 - non_paretic_pos6,
paretic_pos7 - non_paretic_pos7]
processed_reads.append(t)
except ValueError:
pass
l = lbl[0]
for label in range(len(processed_reads)):
if l == 0:
s = [1,0]
else:
s = [0, 1]
processed_labels.append(s)
elif process_id == 2:
for read in batch:
try:
paretic_pos1 = float(read[2])
paretic_pos2 = float(read[3])
paretic_pos3 = float(read[4])
paretic_pos4 = float(read[5])
paretic_pos5 = float(read[6])
paretic_pos6 = float(read[7])
paretic_pos7 = float(read[8])
non_paretic_pos1 = float(read[11])
non_paretic_pos2 = float(read[12])
non_paretic_pos3 = float(read[13])
non_paretic_pos4 = float(read[14])
non_paretic_pos5 = float(read[15])
non_paretic_pos6 = float(read[16])
non_paretic_pos7 = float(read[17])
t = [non_paretic_pos6, paretic_pos6, non_paretic_pos6 - paretic_pos6]
processed_reads.append(t)
except ValueError:
pass
l = lbl[0]
for label in range(len(processed_reads)):
if l == 0:
s = [1,0]
else:
s = [0, 1]
processed_labels.append(s)
elif process_id == 3:
for read in batch:
try:
paretic_pos1 = float(read[2])
paretic_pos2 = float(read[3])
paretic_pos3 = float(read[4])
paretic_pos4 = float(read[5])
paretic_pos5 = float(read[6])
paretic_pos6 = float(read[7])
paretic_pos7 = float(read[8])
non_paretic_pos1 = float(read[11])
non_paretic_pos2 = float(read[12])
non_paretic_pos3 = float(read[13])
non_paretic_pos4 = float(read[14])
non_paretic_pos5 = float(read[15])
non_paretic_pos6 = float(read[16])
non_paretic_pos7 = float(read[17])
t = [paretic_pos1, non_paretic_pos1, paretic_pos1 - non_paretic_pos1, non_paretic_pos6, paretic_pos6, non_paretic_pos6 - paretic_pos6]
processed_reads.append(t)
except ValueError:
pass
l = lbl[0]
for label in range(len(processed_reads)):
if l == 0:
s = [1,0]
else:
s = [0, 1]
processed_labels.append(s)
return processed_reads, processed_labels
a = SinglePatientData("actigraph_reads/DW-001-both_merged.csv", 1, 1, 3)
print(a.get_next_batch())