def create_bags(fname):
B = []
bidx = 0
d = None
N = None
rmode = None
with open(fname, 'r') as ifile:
for ln in ifile:
lns = ln.strip()
if lns == '# Number of Dimensions':
rmode = 'dim'
continue
elif lns == '# Number of Examples':
rmode = 'num'
continue
elif re.match('# Number of Instances of molecule \(\d+\)',
lns) is not None:
molid = int(lns.split('(')[1].split(')')[0])
rmode = 'bag'
continue
elif re.match('# Label of molecule \(\d+\)', lns) is not None:
molid = int(lns.split('(')[1].split(')')[0])
rmode = 'lab'
continue
if rmode == 'dim':
d = int(lns)
continue
if rmode == 'num':
N = int(lns)
continue
if rmode == 'bag':
ni = int(lns)
rmode = 'fea'
X = []
continue
if rmode == 'lab':
assert len(X) == ni * d #ensure correct reading
l = float(lns)
X = np.array(X)
b = Bag()
# b.instances = X.reshape((ni,d))#
b.instances = X.reshape((d, ni)).T # (Amina, look here!)
for bb in b.instances:
np.append(bb, 1.0)
b.label = l
b.id = molid
B.append(b)
b.peta = [1.0] * np.shape(b.instances)[0]
continue
if rmode == 'fea':
X.append(float(lns))
return B
