def test_date(self):
# Test date formatting method.
import time
for i in range(3):
a = time.strftime(myokit.DATE_FORMAT)
b = myokit.date()
if a == b:
break
self.assertEqual(a, b)
def save_atf(log, filename, fields=None):
"""
Saves the :class:`myokit.DataLog` ``log`` to ``filename`` in ATF format.
ATF requires that the times in the log be regularly spaced.
The first column in an ATF file should always be time. Remaining fields
will be written in a random order. To indicate an order or make a selection
of fields, pass in a sequence ``fields`` containing the field names.
"""
log.validate()
import myokit
# Check filename
filename = os.path.expanduser(filename)
# Delimiters
# Dos-style EOL: Open file in 'wb' mode to stop windows writing \r\r\n
eol = '\r\n'
delim = '\t'
# Create data and keys lists
data = [iter(log.time())]
time = log.time_key()
keys = [time]
# Check fields
if fields:
for field in fields:
field = str(field)
if field == time:
continue
keys.append(field)
try:
data.append(iter(log[field]))
except KeyError:
raise ValueError('Variable <' + field + '> not found in log.')
else:
for k, v in log.items():
if k != time:
keys.append(k)
data.append(iter(v))
for k in keys:
if '"' in k:
raise ValueError('Column names must not contain double quotes.')
if '\r' in k or '\n' in k:
raise ValueError(
'Column names must not contain newlines or carriage returns.')
# Check if time is equally spaced
t = np.asarray(log.time())
dt = t[1:] - t[:-1]
dt_ref = dt[0]
dt_err = dt_ref * 1e-6
if np.any(np.abs(dt - dt_ref) > dt_err):
raise ValueError('The time variable must be regularly spaced.')
# Create header
header = []
header.append(('myokit-version', 'Myokit ' + myokit.version(raw=True)))
header.append(('date-created', myokit.date()))
header.append(('sampling-interval', dt_ref))
# Get sizes
nh = len(header)
nf = len(keys)
nd = log.length()
# Write file
with open(filename, 'wb') as f:
# Write version number
f.write(('ATF 1.0' + eol).encode(_ENC))
# Write number of header lines, number of fields
f.write((str(nh) + delim + str(nf) + eol).encode(_ENC))
for k, v in header:
f.write(('"' + str(k) + '=' + str(v) + '"' + eol).encode(_ENC))
# Write field names
f.write((delim.join(['"' + k + '"' for k in keys]) + eol).encode(_ENC))
# Write data
for i in range(nd):
f.write((
delim.join([myokit.strfloat(next(d)) for d in data]) + eol
).encode(_ENC))