def test_equality(self, im):
assert im == IntensityMatrix(im.time_list, im.mass_list,
im.intensity_array)
assert im != test_string
assert im != test_int
assert im != test_float
assert im != test_tuple
assert im != test_list_ints
assert im != test_list_strs
def gcms_sim(
time_list: List[float],
mass_list: List[float],
peak_list: List[Peak.Peak],
) -> IntensityMatrix:
"""
Simulator of GCMS data.
:param time_list: the list of scan times
:param mass_list: the list of m/z channels
:param peak_list: A list of peaks
:return: A simulated Intensity Matrix object
:author: Sean O'Callaghan
"""
n_mz = len(mass_list)
n_scan = len(time_list)
t1 = time_list[0]
period = time_list[1] - t1
# initialise a 2D numpy array for intensity matrix
i_array = numpy.zeros((n_scan, n_mz), 'd')
for peak in peak_list:
print('-', end='')
index = int((peak.rt - t1) / period)
height = sum(peak.mass_spectrum.mass_spec)
# standard deviation = area/(height * sqrt(2/pi))
sigma: float = peak.area / (height *
(math.sqrt(2 * math.pi))) # type: ignore
print("width", sigma)
for i in range(len(peak.mass_spectrum.mass_list)):
ion_height = peak.mass_spectrum.mass_spec[i]
ic = chromatogram(n_scan, index, sigma, ion_height)
i_array[:, i] += ic
im = IntensityMatrix(time_list, mass_list, i_array)
return im
def gcms_sim(time_list: List, mass_list: List,
peak_list: Peak) -> IntensityMatrix:
"""
Simulator of GCMS data
:param time_list: the list of scan times
:type time_list: list
:param mass_list: the list of m/z channels
:type mass_list: list
:param peak_list: A list of peaks
:type peak_list: :class:`list` of :class:`pyms.Peak.Class.Peak` objects
:return: A simulated Intensity Matrix object
:rtype: pyms.IntensityMatrix.IntensityMatrix
:author: Sean O'Callaghan
"""
n_mz = len(mass_list)
n_scan = len(time_list)
t1 = time_list[0]
period = time_list[1] - t1
# initialise a 2D numpy array for intensity matrix
i_array = numpy.zeros((n_scan, n_mz), 'd')
for peak in peak_list:
print("-", end='')
index = int((peak.rt - t1) / period)
height = sum(peak.get_mass_spectrum().mass_spec)
# standard deviation = area/(height * sqrt(2/pi))
sigma = peak.area / (height * (math.sqrt(2 * math.pi)))
print("width", sigma)
for i in range(len(peak.get_mass_spectrum().mass_list)):
ion_height = peak.get_mass_spectrum().mass_spec[i]
ic = chromatogram(n_scan, index, sigma, ion_height)
i_array[:, i] += ic
im = IntensityMatrix(time_list, mass_list, i_array)
return im
def test_intensity_array_errors(self, obj, im, expects):
with pytest.raises(expects):
IntensityMatrix(im.time_list, im.mass_list, obj)
def test_mass_list_errors(self, obj, im, expects):
with pytest.raises(TypeError):
IntensityMatrix(im.time_list, obj, im.intensity_array)
def test_creation(self, im):
assert isinstance(im, IntensityMatrix)
IntensityMatrix(im.time_list, im.mass_list, im.intensity_array)
