def test_scaling(self):
"""
Tests that the chimera data is scaled correctly, from a known test file.
"""
directory = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(directory, 'testDataFiles',
'spheres_20140114_154938_beginning.log')
reader = ChimeraReader(filename)
data = reader.get_all_data()[0]
reader.close()
baseline = np.mean(data)
baseline_should_be = 7.57604 # Value gotten from original MATLAB script
self.assertAlmostEqual(
baseline, baseline_should_be, 2,
"Baseline scaled wrong. Should be {0}, got {1}.".format(
baseline_should_be, baseline))
std = np.std(data)
std_should_be = 1.15445 # Value gotten from original MATLAB script
self.assertAlmostEqual(
std, std_should_be, 2,
"Baseline scaled wrong. Should be {0}, got {1}.".format(
std_should_be, std))
def test_get_all_data(self):
# Make sure path to chimera file is correct.
filename = tf.get_abs_path('chimera_small.log')
chimera_reader = ChimeraReader(filename)
data = chimera_reader.get_all_data(False)
self._test_small_chimera_file_help(data)
chimera_reader.close()
def test_open_chimera_data(self):
# Make sure path to chimera file is correct.
directory = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(os.path.join(directory, 'testDataFiles'), 'smallChimera.log')
chimera_reader = ChimeraReader(filename)
data = chimera_reader.get_all_data(False)
self._test_small_chimera_file_help(data)
chimera_reader.close()
def test_open_chimera_data(self):
# Make sure path to chimera file is correct.
directory = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(os.path.join(directory, 'testDataFiles'),
'smallChimera.log')
chimera_reader = ChimeraReader(filename)
data = chimera_reader.get_all_data(False)
self._test_small_chimera_file_help(data)
chimera_reader.close()
def test_decimate_scaling(self):
"""
Tests that the scaling of the decimated data is the same as the undecimated data.
"""
directory = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(directory, 'testDataFiles', 'spheres_20140114_154938_beginning.log')
reader = ChimeraReader(filename)
data = reader.get_all_data()[0]
data_decimated = reader.get_all_data(decimate=True)[0]
reader.close()
baseline = np.mean(data)
baseline_decimate = np.mean(data_decimated)
self.assertAlmostEqual(baseline, baseline_decimate, 2,
"Decimated baseline scaled wrong. Should be {0}, got {1}.".format(baseline,
baseline_decimate))
def test_scaling(self):
"""
Tests that the chimera data is scaled correctly, from a known test file.
"""
directory = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(directory, 'testDataFiles', 'spheres_20140114_154938_beginning.log')
reader = ChimeraReader(filename)
data = reader.get_all_data()[0]
reader.close()
baseline = np.mean(data)
baseline_should_be = 7.57604 # Value gotten from original MATLAB script
self.assertAlmostEqual(baseline, baseline_should_be, 2,
"Baseline scaled wrong. Should be {0}, got {1}.".format(baseline_should_be, baseline))
std = np.std(data)
std_should_be = 1.15445 # Value gotten from original MATLAB script
self.assertAlmostEqual(std, std_should_be, 2,
"Baseline scaled wrong. Should be {0}, got {1}.".format(std_should_be, std))
def test_decimate_scaling(self):
"""
Tests that the scaling of the decimated data is the same as the undecimated data.
"""
directory = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(directory, 'testDataFiles',
'spheres_20140114_154938_beginning.log')
reader = ChimeraReader(filename)
data = reader.get_all_data()[0]
data_decimated = reader.get_all_data(decimate=True)[0]
reader.close()
baseline = np.mean(data)
baseline_decimate = np.mean(data_decimated)
self.assertAlmostEqual(
baseline, baseline_decimate, 2,
"Decimated baseline scaled wrong. Should be {0}, got {1}.".format(
baseline, baseline_decimate))
def profile_chimera():
filename = tf.get_abs_path('spheres_20140114_154938_beginning.log')
reader = ChimeraReader(filename)
_reader_tasks(reader)
reader.close()