def generate_diagnosis_data():
sid_hadm_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'sid_hadm_dict.json'))
hadm_sid_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'hadm_sid_dict.json'))
hadm_map_dict = dict()
for hadm in hadm_sid_dict:
sid = hadm_sid_dict[hadm]
hadm_list = sid_hadm_dict[sid]
if len(hadm_list) > 1:
hadm_list = sorted(hadm_list, key=lambda k: int(k))
idx = hadm_list.index(hadm)
if idx > 0:
for h in hadm_list[:idx]:
if h not in hadm_map_dict:
hadm_map_dict[h] = []
hadm_map_dict[h].append(hadm)
hadm_icd_dict = dict()
for i_line, line in enumerate(
open(os.path.join(args.mimic_dir, 'DIAGNOSES_ICD.csv'))):
if i_line:
if i_line % 10000 == 0:
print(i_line)
line_data = [x.strip('"') for x in py_op.csv_split(line.strip())]
ROW_ID, SUBJECT_ID, hadm_id, SEQ_NUM, icd = line_data
if hadm_id in hadm_map_dict:
for h in hadm_map_dict[hadm_id]:
if h not in hadm_icd_dict:
hadm_icd_dict[h] = []
hadm_icd_dict[h].append(icd)
hadm_icd_dict = {h: list(set(icds)) for h, icds in hadm_icd_dict.items()}
py_op.mywritejson(os.path.join(args.data_dir, 'hadm_icd_dict.json'),
hadm_icd_dict)
def stat_drug_effect():
for fi in ['train.json', 'valid.json', 'test.json']:
ehr_data = json.load(
open(os.path.join(args.data_dir, args.dataset, fi)))
new_ehr_data = []
has_drug = []
has_hf = [[], []]
for pdata in ehr_data:
patient_dict = pdata[0]
hf = pdata[1]
vis, new_patient_dict = find_drug(patient_dict)
if len(new_patient_dict):
has_drug.append(vis)
has_hf[vis].append(hf)
new_ehr_data.append([new_patient_dict, hf])
print('')
print('In {:s}:'.format(fi.split('.')[0]))
print(
'There are {:d} patients. {:d} patients has drug. {:d} patients hasn\'t drugs.'
.format(len(new_ehr_data), sum(has_drug),
len(ehr_data) - sum(has_drug)))
print(
'Drug patients with hf: {:3.4f}. No drug patients with hf: {:3.4}.'
.format(np.mean(has_hf[1]), np.mean(has_hf[0])))
py_op.mywritejson(
os.path.join(args.data_dir, args.dataset, 'new_' + fi),
new_ehr_data)
def main():
dataset = data_loader.DataBowl(args, phase='train')
train_loader = DataLoader(dataset,
batch_size=args.batch_size,
shuffle=True,
num_workers=args.workers,
pin_memory=True)
dataset = data_loader.DataBowl(args, phase='valid')
valid_loader = DataLoader(dataset,
batch_size=args.batch_size,
shuffle=False,
num_workers=args.workers,
pin_memory=True)
args.vocab = dataset.vocab
args.relation = dataset.relation
# net, loss = model.Net(args), model.Loss()
net, loss = model.FCModel(args), model.Loss()
net = _cuda(net, 0)
loss = _cuda(loss, 0)
parameters_all = []
for p in net.parameters():
parameters_all.append(p)
optimizer = torch.optim.Adam(parameters_all, args.lr)
best_auc = [0, 0, 0, 0, 0, 0]
cui_con_dict = {}
if args.phase == 'train':
for epoch in range(args.epochs):
train(train_loader, net, loss, epoch, optimizer, best_auc)
best_auc, cui_con_dict = test(valid_loader, net, loss, epoch,
best_auc, 'valid', cui_con_dict)
print args.words
if 1:
cons_dir = '../result/cons/{:s}/{:d}'.format(
args.model, args.predict_day)
py_op.mkdir(cons_dir)
num = len(os.listdir(cons_dir))
py_op.mywritejson(os.path.join(cons_dir, '{:d}.json'.format(num)),
cui_con_dict)
# break
print 'best auc', best_auc
auc = best_auc[0]
with open('../result/log.txt', 'a') as f:
f.write('#model {:s} #auc {:3.4f}\n'.format(args.model, auc))
elif args.phase == 'test':
net.load_state_dict(torch.load(args.resume))
test(valid_loader, net, loss, 0, best_auc, 'valid', cui_con_dict)
def generate_icu_mortality_dict(icustay_id_list):
icu_mortality_dict = dict()
for i_line, line in enumerate(
open(os.path.join(args.mimic_dir, 'sepsis_mortality.csv'))):
if i_line:
if i_line % 10000 == 0:
print(i_line)
line_data = line.strip().split(',')
icustay_id = line_data[0]
icu_mortality_dict[icustay_id] = int(line_data[-1])
py_op.mywritejson(os.path.join(args.data_dir, 'icu_mortality_dict.json'),
icu_mortality_dict)
def map_ehr_id():
print('start')
ehr_count_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'ehr_count_dict.json'))
ehr_list = [ehr for ehr, c in ehr_count_dict.items() if c > 100]
ns = set('0123456789')
print(ns)
drug_list = [e for e in ehr_list if e[1] in ns]
med_list = [e for e in ehr_list if e[1] not in ns]
print(len(drug_list))
print(len(med_list))
py_op.mywritejson(os.path.join(args.data_dir, 'ehr_list.json'), ehr_list)
def split_data_to_ten_set():
files = sorted(
glob(os.path.join(args.data_dir, args.dataset,
'train_with_missing/*')))
np.random.shuffle(files)
splits = []
for i in range(10):
st = int(len(files) * i / 10)
en = int(len(files) * (i + 1) / 10)
splits.append(files[st:en])
py_op.mywritejson(
os.path.join(args.file_dir, args.dataset + '_splits.json'), splits)
def compute_pred_clean_psnr(epoch='ensemble',
clean_dir='../../data/AI/testB/',
result_dir='../../data/result'):
psnr_list = []
file_psnr_dict = dict()
if not os.path.exists(result_dir):
os.mkdir(result_dir)
f = open(os.path.join(result_dir, epoch + '.csv'), 'w')
for i, clean in enumerate(os.listdir(clean_dir)):
file = clean
clean = os.path.join(clean_dir, clean)
clean_file = clean
pred = clean.replace('.jpg', '.png').replace(
'data', 'data/test_clean/{:s}'.format(epoch))
stain = clean.replace('trainB', 'trainA').replace('testB',
'testA').replace(
'.jpg', '_.jpg')
try:
pred = Image.open(pred)
pred = pred.resize((256, 256))
pred = pred.resize((250, 250))
pred = np.array(pred).astype(np.float32)
clean = np.array(Image.open(clean)).astype(np.float32)
stain = np.array(Image.open(stain)).astype(np.float32)
psnr_pred = psnr(clean, pred)
psnr_stain = psnr(clean, stain)
psnr_list.append([psnr_stain, psnr_pred])
file_psnr_dict[file] = psnr_pred
except:
traceback.print_exc()
continue
print i, 1000
f.write(clean_file.split('/')[-1])
f.write(',')
f.write(str(psnr_stain))
f.write(',')
f.write(str(psnr_pred))
f.write(',')
f.write(str(psnr_pred / psnr_stain - 1))
f.write('\n')
psnr_list = np.array(psnr_list)
psnr_mean = ((psnr_list[:, 1] - psnr_list[:, 0]) / psnr_list[:, 0]).mean()
f.write(str(psnr_mean))
f.close()
py_op.mywritejson(
os.path.join(result_dir, epoch + '.json'),
py_op.mysorteddict(file_psnr_dict, key=lambda s: file_psnr_dict[s]))
print '网纹图PSNR', psnr_list[:, 0].mean()
print '预测图PSNR', psnr_list[:, 1].mean()
print '增益率', psnr_mean
return psnr_mean
def generate_ehr_files():
hadm_time_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'hadm_time_dict.json'))
hadm_demo_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'hadm_demo_dict.json'))
hadm_sid_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'hadm_sid_dict.json'))
hadm_icd_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'hadm_icd_dict.json'))
hadm_time_drug_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'hadm_time_drug_dict.json'))
groundtruth_dir = os.path.join(args.data_dir, 'train_groundtruth')
py_op.mkdir(groundtruth_dir)
ehr_count_dict = dict()
for hadm_id in hadm_sid_dict:
time_drug_dict = hadm_time_drug_dict.get(hadm_id, {})
icd_list = hadm_icd_dict.get(hadm_id, [])
demo = hadm_demo_dict[hadm_id]
demo[0] = demo[0] + '1'
demo[1] = 'A' + str(int(demo[1] / 9))
icd_demo = icd_list + demo
for icd in icd_demo:
ehr_count_dict[icd] = ehr_count_dict.get(icd, 0) + 1
ehr_dict = {'drug': {}, 'icd_demo': icd_demo}
for setime, drug_list in time_drug_dict.items():
try:
stime, etime = setime.split(' -- ')
start_second = time_to_second(hadm_time_dict[hadm_id])
stime = str((time_to_second(stime) - start_second) / 3600)
etime = str((time_to_second(etime) - start_second) / 3600)
setime = stime + ' -- ' + etime
for drug in drug_list:
ehr_count_dict[drug] = ehr_count_dict.get(drug, 0) + 1
ehr_dict['drug'][setime] = list(set(drug_list))
except:
pass
py_op.mywritejson(os.path.join(groundtruth_dir, hadm_id + '.json'),
ehr_dict)
# break
py_op.mywritejson(os.path.join(args.data_dir, 'ehr_count_dict.json'),
ehr_count_dict)
def generate_feature_mm_dict():
files = sorted(
glob(os.path.join(args.data_dir, args.dataset, 'train_groundtruth/*')))
feature_value_dict = dict()
for ifi, fi in enumerate(tqdm(files)):
if 'csv' not in fi:
continue
for iline, line in enumerate(open(fi)):
line = line.strip()
if iline == 0:
feat_list = line.split(',')
else:
data = line.split(',')
for iv, v in enumerate(data):
if v in ['NA', '']:
continue
else:
feat = feat_list[iv]
if feat not in feature_value_dict:
feature_value_dict[feat] = []
feature_value_dict[feat].append(float(v))
feature_mm_dict = dict()
feature_ms_dict = dict()
feature_range_dict = dict()
for feat, vs in feature_value_dict.items():
vs = sorted(vs)
value_split = []
for i in range(args.split_num):
n = int(i * len(vs) / args.split_num)
value_split.append(vs[n])
value_split.append(vs[-1])
feature_range_dict[feat] = value_split
n = int(len(vs) / args.split_num)
feature_mm_dict[feat] = [vs[n], vs[-n - 1]]
feature_ms_dict[feat] = [np.mean(vs), np.std(vs)]
py_op.mkdir(args.file_dir)
py_op.mywritejson(
os.path.join(args.file_dir, args.dataset + '_feature_mm_dict.json'),
feature_mm_dict)
py_op.mywritejson(
os.path.join(args.file_dir, args.dataset + '_feature_ms_dict.json'),
feature_ms_dict)
py_op.mywritejson(
os.path.join(args.file_dir, args.dataset + '_feature_list.json'),
feat_list)
py_op.mywritejson(
os.path.join(
args.file_dir, args.dataset +
'_feature_value_dict_{:d}.json'.format(args.split_num)),
feature_range_dict)
def wkmeans(n_cluster):
subtyping_dir = os.path.join(args.result_dir, args.dataset, 'subtyping')
hadm_id_list = py_op.myreadjson(os.path.join(subtyping_dir, 'hadm_id_list.json'))
hadm_dist_matrix = np.load(os.path.join(subtyping_dir, 'hadm_dist_matrix.npy'))
assert len(hadm_dist_matrix) == len(hadm_id_list)
# initialization
indices = range(len(hadm_id_list))
np.random.shuffle(indices)
init_groups = [indices[i*10: i*10 + 10] for i in range(n_cluster)]
groups = init_groups
for epoch in range(100):
groups = wkmeans_epoch(hadm_dist_matrix, groups)
print([len(g) for g in groups])
if epoch and epoch % 10 == 0:
cluster_results = []
for g in groups:
cluster_results.append([hadm_id_list[i] for i in g])
py_op.mywritejson(os.path.join(subtyping_dir, 'cluster_results.json'), cluster_results)
def generate_drug_data():
hadm_sid_dict = py_op.myreadjson(
os.path.join(args.data_dir, 'hadm_sid_dict.json'))
hadm_id_set = set(hadm_sid_dict)
hadm_time_drug_dict = dict()
for i_line, line in enumerate(
open(os.path.join(args.mimic_dir, 'PRESCRIPTIONS.csv'))):
if i_line:
if i_line % 10000 == 0:
print(i_line)
line_data = [x.strip('"') for x in py_op.csv_split(line.strip())]
_, SUBJECT_ID, hadm_id, _, startdate, enddate, _, drug, DRUG_NAME_POE, DRUG_NAME_GENERIC, FORMULARY_DRUG_CD, gsn, ndc, PROD_STRENGTH, DOSE_VAL_RX, DOSE_UNIT_RX, FORM_VAL_DISP, FORM_UNIT_DISP, ROUTE = line_data
if len(hadm_id) and hadm_id in hadm_id_set:
if hadm_id not in hadm_time_drug_dict:
hadm_time_drug_dict[hadm_id] = dict()
time = startdate + ' -- ' + enddate
if time not in hadm_time_drug_dict[hadm_id]:
hadm_time_drug_dict[hadm_id][time] = []
hadm_time_drug_dict[hadm_id][time].append(drug)
# hadm_time_drug_dict[hadm_id][time].append(ndc)
py_op.mywritejson(os.path.join(args.data_dir, 'hadm_time_drug_dict.json'),
hadm_time_drug_dict)
def generate_demo():
icu_hadm_dict = py_op.myreadjson('../../src/icu_hadm_dict.json')
py_op.mywritejson(os.path.join(args.data_dir, 'icu_hadm_dict.json'),
icu_hadm_dict)
sid_demo_dict = dict()
sid_hadm_dict = dict()
for i_line, line in enumerate(
open(os.path.join(args.mimic_dir, 'PATIENTS.csv'))):
if i_line:
data = line.split(',')
sid = data[1]
gender = data[2].replace('"', '')
dob = data[3][:4]
sid_demo_dict[sid] = [gender, int(dob)]
py_op.mywritejson(os.path.join(args.data_dir, 'sid_demo_dict.json'),
sid_demo_dict)
hadm_sid_dict = dict()
hadm_demo_dict = dict()
hadm_time_dict = dict()
for i_line, line in enumerate(
open(os.path.join(args.mimic_dir, 'ICUSTAYS.csv'))):
if i_line:
line = line.replace('"', '')
data = line.split(',')
sid = data[1]
hadm_id = data[2]
icu_id = data[3]
intime = data[-3]
sid_hadm_dict[sid] = sid_hadm_dict.get(sid, []) + [hadm_id]
if icu_id not in icu_hadm_dict:
continue
hadm_sid_dict[hadm_id] = sid
gender = sid_demo_dict[sid][0]
dob = sid_demo_dict[sid][1]
age = int(intime[:4]) - dob
if age < 18:
print(age)
assert age >= 18
if age > 150:
age = 90
hadm_demo_dict[hadm_id] = [gender, age]
hadm_time_dict[hadm_id] = intime
py_op.mywritejson(os.path.join(args.data_dir, 'hadm_demo_dict.json'),
hadm_demo_dict)
py_op.mywritejson(os.path.join(args.data_dir, 'hadm_time_dict.json'),
hadm_time_dict)
py_op.mywritejson(os.path.join(args.data_dir, 'sid_hadm_dict.json'),
sid_hadm_dict)
py_op.mywritejson(os.path.join(args.data_dir, 'hadm_sid_dict.json'),
hadm_sid_dict)
def compute_dist_mat():
files = glob(
os.path.join(args.result_dir, args.dataset,
'imputation_result/*.csv')) # [:100]
feature_ms_dict = py_op.myreadjson(
os.path.join(args.file_dir, args.dataset + '_feature_ms_dict.json'))
subtyping_dir = os.path.join(args.result_dir, args.dataset, 'subtyping')
py_op.mkdir(subtyping_dir)
hadm_id_list = []
mean_variables = []
hadm_variable_dict = {}
all_values = []
for i_fi, fi in enumerate(tqdm(files)):
hadm_id = fi.split('/')[-1].split('.')[0]
hadm_data = []
for i_line, line in enumerate(open(fi)):
if i_line:
line_data = line.strip().split(',')
line_data = np.array([float(x) for x in line_data])
if len(line_data) != n_variables + 1:
print(i_fi, fi)
if line_data[0] < 0:
continue
elif line_data[0] < 24:
hadm_data.append(line_data)
else:
break
else:
head = line.strip().split(',')[1:]
assert len(head) == n_variables
values = np.array(hadm_data, dtype=np.float32)
values = values[-24:]
times = values[:, 0]
values = values[:, 1:]
assert len(values.shape) == 2
assert values.shape[1] == n_variables
hadm_variable_dict[hadm_id] = values
hadm_id_list.append(hadm_id)
all_values.append(values)
all_values = np.concatenate(all_values, 0)
ms = [all_values.mean(0), all_values.std(0)]
hadm_dist_matrix = np.zeros((len(hadm_id_list), len(hadm_id_list))) - 1
for i in tqdm(range(len(hadm_id_list))):
hadm_dist_matrix[i, i] = 0
for j in range(i + 1, len(hadm_id_list)):
if hadm_dist_matrix[i, j] >= 0 or i == j:
continue
s1 = hadm_variable_dict[hadm_id_list[i]]
s2 = hadm_variable_dict[hadm_id_list[j]]
s1 = norm(s1, ms)
s2 = norm(s2, ms)
dist_mat = dist_func(s1, s2)
path = np.zeros([dist_mat.shape[0], dist_mat.shape[1], 3
]) - inf - 1
compute_dtw(dist_mat, path, hadm_dist_matrix, i, j)
py_op.mywritejson(os.path.join(subtyping_dir, 'hadm_id_list.json'),
hadm_id_list)
np.save(os.path.join(subtyping_dir, 'hadm_dist_matrix.npy'),
hadm_dist_matrix)
