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Deal with yet another format - with more flags data (I think)

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Chris Kerr
2013-12-08 14:07:32 +00:00
parent fa14ba94f8
commit 509b75a81f
2 changed files with 47 additions and 11 deletions
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45
BioLogic.py
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@@ -135,6 +135,13 @@ VMPdata_dtype = np.dtype([('flags', 'u1'),
("Ewe/V", '<f4'), ("Ewe/V", '<f4'),
("dQ/mA.h", '<f8'), ("dQ/mA.h", '<f8'),
("P/W", '<f4')]) ("P/W", '<f4')])
VMPdata_dtype_extra = np.dtype([('flags', '<u2'),
('blank', 'a1'),
("time/s", '<f8'),
("control/V/mA", '<f4'),
("Ewe/V", '<f4'),
("dQ/mA.h", '<f8'),
("P/W", '<f4')])
def read_VMP_modules(fileobj, read_module_data=True): def read_VMP_modules(fileobj, read_module_data=True):
@@ -211,27 +218,47 @@ class MPRfile:
n_columns = int(data_module['data'][4]) n_columns = int(data_module['data'][4])
if data_module['version'] == 0: if data_module['version'] == 0:
## There is 100 bytes of data before the main array starts ## There is 100 bytes of data before the main array starts
assert(n_columns == 11)
column_types = np.fromstring(data_module['data'][5:], dtype='u1', column_types = np.fromstring(data_module['data'][5:], dtype='u1',
count=n_columns) count=n_columns)
np.testing.assert_array_equal(column_types,
[1, 2, 3, 21, 31, 65,
4, 5, 6, 7, 70])
assert(data_module['length'] - 100 == assert(data_module['length'] - 100 ==
VMPdata_dtype.itemsize * n_data_points) VMPdata_dtype.itemsize * n_data_points)
self.data = np.frombuffer(data_module['data'], dtype=VMPdata_dtype, self.data = np.frombuffer(data_module['data'],
dtype=VMPdata_dtype,
offset=100) offset=100)
elif data_module['version'] == 2: elif data_module['version'] == 2:
## There is 405 bytes of data before the main array starts ## There is 405 bytes of data before the main array starts
column_types = np.fromstring(data_module['data'][5:], dtype='<u2', column_types = np.fromstring(data_module['data'][5:], dtype='<u2',
count=n_columns) count=n_columns)
assert(data_module['length'] - 405 == if n_columns == 11:
VMPdata_dtype.itemsize * n_data_points) np.testing.assert_array_equal(column_types,
self.data = np.frombuffer(data_module['data'], dtype=VMPdata_dtype, [1, 2, 3, 21, 31, 65,
offset=405) 4, 5, 6, 7, 70])
assert(data_module['length'] - 405 ==
VMPdata_dtype.itemsize * n_data_points)
self.data = np.frombuffer(data_module['data'],
dtype=VMPdata_dtype,
offset=405)
elif n_columns == 12:
np.testing.assert_array_equal(column_types,
[1, 2, 3, 21, 31, 65,
131, 4, 5, 6, 7, 70])
assert(data_module['length'] - 405 ==
VMPdata_dtype_extra.itemsize * n_data_points)
self.data = np.frombuffer(data_module['data'],
dtype=VMPdata_dtype_extra,
offset=405)
assert(np.all(self.data['blank'] == b'\x00'))
else:
raise ValueError("Cannot deal with n_columns = %d" % n_columns)
else: else:
raise ValueError("Unrecognised version for data module: %d" % raise ValueError("Unrecognised version for data module: %d" %
data_module['version']) data_module['version'])
## No idea what these 'column types' mean or even if they are actually ## No idea what these 'column types' mean or even if they are actually
## column types at all ## column types at all
np.testing.assert_array_equal(column_types,
[1, 2, 3, 21, 31, 65, 4, 5, 6, 7, 70])
tm = time.strptime(str(settings_mod['date'], encoding='ascii'), tm = time.strptime(str(settings_mod['date'], encoding='ascii'),
'%m/%d/%y') '%m/%d/%y')

13
tests/test_BioLogic.py
View File

@@ -41,18 +41,27 @@ def test_open_MPT_csv_fails_for_bad_file():
mpt1 = MPTfileCSV(os.path.join(testdata_dir, 'bio-logic1.mpr')) mpt1 = MPTfileCSV(os.path.join(testdata_dir, 'bio-logic1.mpr'))
def test_MPR1_read_dates(): def test_open_MPR1():
mpr1 = MPRfile(os.path.join(testdata_dir, 'bio-logic1.mpr')) mpr1 = MPRfile(os.path.join(testdata_dir, 'bio-logic1.mpr'))
## Check the dates as a basic test that it has been read properly
eq_(mpr1.startdate, date(2011, 10, 29)) eq_(mpr1.startdate, date(2011, 10, 29))
eq_(mpr1.enddate, date(2011, 10, 31)) eq_(mpr1.enddate, date(2011, 10, 31))
def test_MPR2_read_dates(): def test_open_MPR2():
mpr2 = MPRfile(os.path.join(testdata_dir, 'bio-logic2.mpr')) mpr2 = MPRfile(os.path.join(testdata_dir, 'bio-logic2.mpr'))
## Check the dates as a basic test that it has been read properly
eq_(mpr2.startdate, date(2012, 9, 27)) eq_(mpr2.startdate, date(2012, 9, 27))
eq_(mpr2.enddate, date(2012, 9, 27)) eq_(mpr2.enddate, date(2012, 9, 27))
def test_open_MPR3():
mpr2 = MPRfile(os.path.join(testdata_dir, 'bio-logic3.mpr'))
## Check the dates as a basic test that it has been read properly
eq_(mpr2.startdate, date(2013, 3, 27))
eq_(mpr2.enddate, date(2013, 3, 27))
@raises(ValueError) @raises(ValueError)
def test_open_MPR_fails_for_bad_file(): def test_open_MPR_fails_for_bad_file():
mpr1 = MPRfile(os.path.join(testdata_dir, 'arbin1.res')) mpr1 = MPRfile(os.path.join(testdata_dir, 'arbin1.res'))