import matplotlib.pyplot as plt from sklearn import svm from sklearn.linear_model import LogisticRegression as LR from sklearn.neighbors import KNeighborsClassifier as KNC from xgboost import XGBClassifier as XGBC from sklearn.decomposition import PCA from sklearn.naive_bayes import GaussianNB as GNB import pywt, csv #CHANNEL_IND = channels[ind_ds] # data_set = 'ecgiddb' # 'ecgiddb', 'mitdb' channel = 1 records, labels, fss = mf.load_data(data_set, channel, num_persons=30, record_time=20) USE_BIOSPPY_FILTERED = True segs_all, labels_all = mf.get_seg_data(records, labels, fss, USE_BIOSPPY_FILTERED) methods_feat = ['DL'] #ind_fts = 0 #method_feat = 'orig' #method_feats[ind_fts] methods_clsf = ['Logit', 'GNB', 'kNN', 'SVC', 'boosting', 'DL'] #ind_cls = 0 #method_clsf = 'Logit' #methods_clsfy[ind_cls] num_feats = len(methods_feat) num_clsfy = len(methods_clsf)
def optimCurveFit(strategy, method_clsf, ratio=0.8, NV_type='NVequals'):
constrain_time = True
######################
#TODO Step 1: Data input
######################
data_set = 'mitdb' # 'ecgiddb', 'mitdb'
channel = 0
records, IDs, fss, annss = mf.load_data(
data_set, channel) #, num_persons=60, record_time=20)
fs = fss[0]
records = np.array(records)
IDs = np.array(IDs)
annss = np.array(annss)
######################
######################
#TODO Step 2: Data selection
######################
if (strategy == 'allN_data') or (strategy == 'all_data'):
'' # do nothing here
elif strategy == 'NV_data':
NV_inds = [6, 15, 18, 23, 24, 26, 29, 31, 33, 35, 39, 41, 42, 46]
#for i in NV_inds: #range(annss.shape[0]): #
# print i, Counter(annss[i][1])['V']
records = records[NV_inds, :]
IDs = IDs[NV_inds]
annss = annss[NV_inds, :]
## re-numbering the IDs... wtf
for i in range(len(NV_inds)):
IDs[i] = i
elif strategy == 'combine_IDs':
num_to_combine = 4
print IDs
for i in range(int(len(records) / num_to_combine)):
for j in range(num_to_combine - 1):
IDs[i * num_to_combine + j + 1] = IDs[i * num_to_combine + j]
#IDs[i*2+1] = IDs[i*2]
for i in range(len(IDs)):
IDs[i] /= num_to_combine
if constrain_time:
look_time = 600. # in s
look_ind = int(look_time * fs)
records = records[:, :look_ind]
annss = annss[:, :look_ind]
recs = []
for i in range(len(records)):
curr_rec = Rec(records[i], fs, IDs[i], annss[i])
recs.append(curr_rec)
######################
######################
#TODO Step 3: Data filtering
######################
######################
######################
#TODO Step 4: Data segmentation
######################
USE_BIOSPPY_FILTERED = True
sigs, labels_bySegs = mf.get_seg_data(records,
IDs,
fss,
USE_BIOSPPY_FILTERED,
annss=annss)
sigs, labels_bySegs = np.array(sigs), np.array(labels_bySegs)
mrks_bySegs = np.array([x[-1] for x in labels_bySegs])
if strategy == 'allN_data':
N_masks = (mrks_bySegs == 'N')
sigs = sigs[N_masks, :]
labels_bySegs = labels_bySegs[N_masks]
IDs_bySegs = [int(x[:-1]) for x in labels_bySegs]
mrks_bySegs = [x[-1] for x in labels_bySegs]
IDs_bySegs, mrks_bySegs = np.array(IDs_bySegs), np.array(mrks_bySegs)
segs = []
for i in range(len(sigs)):
curr_seg = Seg(sig=sigs[i],
fs=fs,
ID=IDs_bySegs[i],
mrk=mrks_bySegs[i])
segs.append(curr_seg)
segs = np.array(segs)
######################
#for one_label in labels_all:
# if ('N' in one_label) or ('V' in one_label):
# print one_label
#quit()
#segs_all, labels_all = np.array(segs_all), np.array(labels_all)
######################
#TODO Step 5: feature extraction
######################
X_all = []
y_all = []
method_feat = 'PCA' # 'template_matching'
if method_feat == 'PCA':
feat_dim = 20
pca = PCA(n_components=feat_dim)
X_all = np.array([x.sig for x in segs])
X_all = pca.fit(X_all).transform(X_all)
for i in range(len(segs)):
segs[i].feat = X_all[i, :]
y_all = np.array([x.ID for x in segs])
X_all = np.array(X_all)
######################
######################
#TODO Step 6: Data split
######################
if strategy != 'NV_data':
X_train, X_test, y_train, y_test = train_test_split(X_all,
y_all,
test_size=0.2,
random_state=42)
else:
X_train, X_test, y_train, y_test = [], [], [], []
y_test_mrks = []
for i in range(len(NV_inds)):
curr_mrks = mrks_bySegs[IDs_bySegs == i] #current people's mrks\
#print curr_mrks
curr_segs = segs[IDs_bySegs == i]
curr_labels = labels_bySegs[IDs_bySegs == i]
curr_inds_Vs = np.where(curr_mrks == 'V')[0]
curr_inds_Ns = np.where(curr_mrks == 'N')[0]
curr_num_Vs = sum(np.array(curr_mrks) == 'V') #all his Vs
curr_num_Ns = sum(np.array(curr_mrks) == 'N')
if NV_type == 'fixV':
train_num_Vs = int(curr_num_Vs * .8)
train_num_Ns = min(
[int(curr_num_Ns * .8),
int(ratio * train_num_Vs)])
elif NV_type == 'NVequals':
train_num_Vs = int(curr_num_Vs * ratio)
train_num_Ns = train_num_Vs
train_inds_Vs = random.sample(curr_inds_Vs, train_num_Vs)
test_inds_Vs = [
x for x in curr_inds_Vs if not (x in train_inds_Vs)
]
#test_inds_Vs = curr_inds_Vs[~ train_inds_Vs]
train_inds_Ns = random.sample(curr_inds_Ns, train_num_Ns)
test_inds_Ns = [
x for x in curr_inds_Ns if not (x in train_inds_Ns)
]
#print len(train_inds_Vs), len(test_inds_Vs)
#print len(train_inds_Ns), len(test_inds_Ns)
#test_inds_Ns = curr_inds_Vs[~ train_inds_Ns]
# print train_inds_Ns
# print test_inds_Ns
curr_IDs = IDs_bySegs[IDs_bySegs == i]
#print curr_IDs
for one_seg in curr_segs[train_inds_Vs]:
X_train.append(one_seg.feat.tolist())
for one_lab in curr_IDs[train_inds_Vs]:
y_train.append(one_lab)
for one_seg in curr_segs[train_inds_Ns]:
X_train.append(one_seg.feat.tolist())
for one_lab in curr_IDs[train_inds_Ns]:
y_train.append(one_lab)
for one_seg in curr_segs[test_inds_Vs]:
X_test.append(one_seg.feat.tolist())
for one_lab in curr_IDs[test_inds_Vs]:
y_test.append(one_lab)
for one_mrk in curr_mrks[test_inds_Vs]:
y_test_mrks.append(one_mrk)
for one_seg in curr_segs[test_inds_Ns]:
X_test.append(one_seg.feat.tolist())
for one_lab in curr_IDs[test_inds_Ns]:
y_test.append(one_lab)
for one_mrk in curr_mrks[test_inds_Ns]:
y_test_mrks.append(one_mrk)
#print i
#print len(X_train), len(y_train), len(X_test), len(y_test)
X_train, y_train, X_test, y_test = \
np.array(X_train), np.array(y_train), np.array(X_test), np.array(y_test)
######################
#print X_train.shape, y_train.shape, X_test.shape, y_test.shape
#quit()
#print X_train
#print X_test
#y_train = [int(y[:-1]) for y in y_train]
#y_test = [int(y[:-1]) for y in y_test]
######################
#TODO Step 7: Model training
######################
time_before_training = Time()
if method_clsf == 'SVM':
not_trained = True
from sklearn.externals import joblib
if not_trained:
clf = svm.SVC(kernel='rbf', C=10., gamma=0.1)
clf.fit(X_train, y_train)
joblib.dump(clf, 'test_clf.pkl')
else:
clf = joblib.load('test_clf.pkl')
res_pred = clf.predict(X_test)
elif method_clsf == 'Logit':
clf = LR(C=10.)
clf.fit(X_train, y_train)
res_pred = clf.predict(X_test)
elif method_clsf == 'kNN':
clf = KNC()
clf.fit(X_train, y_train)
res_pred = clf.predict(X_test)
elif method_clsf == 'DTC':
clf = DTC()
clf.fit(X_train, y_train)
res_pred = clf.predict(X_test)
elif method_clsf == 'boosting':
clf = XGBC()
clf.fit(X_train, y_train)
res_pred = clf.predict(X_test)
elif method_clsf == 'GNB':
clf = GNB()
clf.fit(X_train, y_train)
res_pred = clf.predict(X_test)
elif method_clsf == 'DL':
not_trained = True
from sklearn.externals import joblib
if not_trained:
model = Sequential()
model.add(
Dense(feat_dim, activation='relu', input_shape=(feat_dim, )))
#model.add(Dense(input_dim,activation='relu'))
num_categs = len(set(y_train))
print y_train, num_categs
Y_train = np_utils.to_categorical(y_train, num_categs)
Y_test = np_utils.to_categorical(y_test, num_categs)
model.add(Dense(num_categs, activation='softmax'))
model.compile(loss='categorical_crossentropy',
optimizer='adam',
metrics=['accuracy'])
X_train = np.array(X_train)
Y_train = np.array(Y_train)
#print X_train.shape
#print Y_train.shape
model.fit(X_train,
Y_train,
validation_split=0.2,
batch_size=32,
nb_epoch=50,
verbose=0)
#model.save('test_clf_DL.pkl')
else:
model = keras.models.load_model('test_clf_DL.pkl')
#score = model.evaluate(X_test, Y_test, verbose=0)
time_after_training = Time()
######################
#TODO Step 8: Model testing
######################
if method_clsf != 'DL':
res_pred = clf.predict(X_test)
else:
res_pred = model.predict_classes(X_test)
######################
######################
#TODO Step 9: Result output
######################
train_time = time_after_training - time_before_training
print_res = False
if print_res:
print ''
print 'Parameters:'
print 'strategy:', strategy
print 'constrain_time:', constrain_time
print 'ratio:', ratio
print 'method_clsf:', method_clsf
#print ''
print 'Results:'
print 'Used time for training:', time_after_training - time_before_training
res_look = []
for i in range(len(res_pred)):
res_look.append((res_pred[i], y_test[i]))
#print res_look
if False:
res_pred_IDs = np.array([y[:-1] for y in res_pred])
res_pred_mrks = np.array([y[-1] for y in res_pred])
only_test_ID = True
if only_test_ID:
to_be_predct = res_pred_IDs
to_be_tested = y_test
else:
to_be_predct = res_pred
to_be_tested = y_test
##TODO: adjust accordingly
if strategy == 'NV_data':
look_stat = 'V'
y_test_mrks = np.array(y_test_mrks)
#print y_test_mrks
to_be_predct = res_pred[y_test_mrks == look_stat]
to_be_tested = y_test[y_test_mrks == look_stat]
res_by_seg = mf.get_corr_ratio(res_pred=to_be_predct,
y_test=to_be_tested,
type='by_seg')
res_by_categ = mf.get_corr_ratio(res_pred=to_be_predct,
y_test=to_be_tested,
type='by_categ')
one_res = (float(format(res_by_seg,
'.3f')), float(format(res_by_categ, '.3f')))
accuBySeg_V = one_res[0]
#print len(to_be_predct), one_res
look_stat = 'N'
to_be_predct = res_pred[y_test_mrks == look_stat]
to_be_tested = y_test[y_test_mrks == look_stat]
res_by_seg = mf.get_corr_ratio(res_pred=to_be_predct,
y_test=to_be_tested,
type='by_seg')
res_by_categ = mf.get_corr_ratio(res_pred=to_be_predct,
y_test=to_be_tested,
type='by_categ')
one_res = (float(format(res_by_seg,
'.3f')), float(format(res_by_categ, '.3f')))
accuBySeg_N = one_res[0]
#print len(to_be_predct), one_res
return [accuBySeg_V, accuBySeg_N, train_time]
else:
to_be_predct = res_pred
to_be_tested = y_test
res_by_seg = mf.get_corr_ratio(res_pred=to_be_predct,
y_test=to_be_tested,
type='by_seg')
res_by_categ = mf.get_corr_ratio(res_pred=to_be_predct,
y_test=to_be_tested,
type='by_categ')
one_res = (float(format(res_by_seg,
'.3f')), float(format(res_by_categ, '.3f')))
return [one_res[0], train_time]
import my_funcs as mf
import numpy as np
from collections import Counter
import time
start_time = time.time()
print 1 != 2
data_set = 'mitdb' # 'ecgiddb', 'mitdb'
channel = 0
records, IDs, fss, annss = mf.load_data(
data_set, channel) #, num_persons=60, record_time=20)
fs = fss[0]
records = np.array(records)
IDs = np.array(IDs)
annss = np.array(annss)
for i in range(annss.shape[0]): #
print i, Counter(annss[i][1])
print time.time() - start_time
from sklearn import svm
from sklearn.linear_model import LogisticRegression as LR
from sklearn.neighbors import KNeighborsClassifier as KNC
from xgboost import XGBClassifier as XGBC
from sklearn.decomposition import PCA
from sklearn.naive_bayes import GaussianNB as GNB
import pywt, csv
#CHANNEL_IND = channels[ind_ds] #
data_set = 'ecgiddb' # 'ecgiddb', 'mitdb'
channel = 1
num_persons = 10
records, labels, fss = mf.load_data(data_set, channel, num_persons=num_persons)
USE_BIOSPPY_FILTERED = True
segs_all, labels_all = mf.get_seg_data(records, labels, fss,
USE_BIOSPPY_FILTERED)
print 'method_feat: ' + 'orig' + ', method_clsfy: ' + 'DL'
X_all, y_all = np.array(segs_all), np.array(labels_all)
feat_dim = X_all.shape[1]
X_train, X_test, y_train, y_test = train_test_split(X_all,
y_all,
test_size=0.2,
random_state=42)
