def test_IonChromatogram(im, tic):
# get the first ion chromatogram of the IntensityMatrix
ic = im.get_ic_at_index(0)
assert isinstance(ic, IonChromatogram)
assert not ic.is_tic()
# get the ion chromatogram for m/z = 73
ic = im.get_ic_at_mass(73)
assert isinstance(ic, IonChromatogram)
assert not ic.is_tic()
assert isinstance(tic, IonChromatogram)
assert tic.is_tic()
# Errors
for obj in [test_string, *test_numbers, *test_sequences, test_dict]:
with pytest.raises(TypeError):
IonChromatogram(obj, tic.time_list)
for obj in [test_string, *test_numbers, test_list_strs, test_dict]:
with pytest.raises(TypeError):
IonChromatogram(tic.intensity_array, obj)
for obj in [test_string, *test_sequences, test_dict]:
with pytest.raises(TypeError):
IonChromatogram(tic.intensity_array, tic.time_list, mass=obj)
with pytest.raises(ValueError):
IonChromatogram(tic.intensity_array, test_list_ints)
def get_ic_at_index(self, ix):
"""
Returns the ion chromatogram at the specified index
:param ix: Index of an ion chromatogram in the intensity data
matrix
:type ix: int
:return: Ion chromatogram at given index
:rtype: pyms.IonChromatogram.IonChromatogram
:authors: Qiao Wang, Andrew Isaac, Vladimir Likic
"""
if not isinstance(ix, int):
raise TypeError("'ix' must be an integer")
ia = []
for i in range(len(self._intensity_array)):
ia.append(self._intensity_array[i][ix])
ic_ia = numpy.array(ia)
mass = self.get_mass_at_index(ix)
rt = copy.deepcopy(self._time_list)
return IonChromatogram(ic_ia, rt, mass)
def test_equality(tic, im):
assert tic == IonChromatogram(tic.intensity_array, tic.time_list)
assert tic != im.get_ic_at_index(0)
assert tic != test_string
assert tic != test_int
assert tic != test_float
assert tic != test_list_ints
assert tic != test_list_strs
assert tic != test_dict
assert tic != test_tuple
def tic(self) -> IonChromatogram: """ Returns the TIC of the intensity matrix. .. versionadded:: 2.3.0 """ intensity_list = [] for i in range(len(self._intensity_array)): intensity_list.append(sum(self._intensity_array[i])) return IonChromatogram(numpy.array(intensity_list), self._time_list[:], None)
def test_intensity_array(tic, im): tic = copy.deepcopy(tic) assert isinstance(tic.intensity_array, numpy.ndarray) assert all(numpy.equal(IonChromatogram(tic.intensity_array, tic.time_list).intensity_array, tic.intensity_array)) ic = im.get_ic_at_index(0) tic.intensity_array = ic.intensity_array assert all(numpy.equal(tic.intensity_array, ic.intensity_array)) assert isinstance(tic.intensity_array, numpy.ndarray) assert isinstance(tic.intensity_array[0], float) assert tic.intensity_array[0] == 0.0 assert tic.intensity_array[2] == 622.0
def _calc_tic(self) -> None:
"""
Calculate the total ion chromatogram.
:authors: Qiao Wang, Andrew Isaac, Vladimir Likic
"""
intensities = []
for scan in self._scan_list:
intensities.append(sum(scan.intensity_list))
ia = numpy.array(intensities)
rt = copy.deepcopy(self._time_list)
tic = IonChromatogram(ia, rt)
self._tic = tic
def test_success(self, im, tic):
# get the first ion chromatogram of the IntensityMatrix
ic = im.get_ic_at_index(0)
assert isinstance(ic, IonChromatogram)
assert not ic.is_tic()
# get the ion chromatogram for m/z = 73
ic = im.get_ic_at_mass(73)
assert isinstance(ic, IonChromatogram)
assert not ic.is_tic()
assert isinstance(tic, IonChromatogram)
assert tic.is_tic()
with pytest.raises(
ValueError,
match="'intensity_list' and 'time_list' differ in length"):
IonChromatogram(tic.intensity_array, test_list_ints)
def sum_maxima(im: IntensityMatrix,
points: int = 3,
scans: int = 1) -> IonChromatogram:
"""
Reconstruct the TIC as sum of maxima
:param im: An :class:`~pyms.IntensityMatrix.IntensityMatrix` object
:type im: ~pyms.IntensityMatrix.IntensityMatrix
:param points: Peak if maxima over 'points' number of scans. Default ``3``
:type points: int, optional
:param scans: Number of scans to combine peaks from to compensate for spectra skewing. Default ``1``
:type scans: int, optional
:return: The reconstructed TIC
:rtype: ~pyms.IonChromatogram.IonChromatogram
:author: Andrew Isaac, Dominic Davis-Foster (type assertions)
"""
if not isinstance(im, IntensityMatrix):
raise TypeError("'im' must be an IntensityMatrix object")
if not isinstance(points, int):
raise TypeError("'points' must be an integer")
if not isinstance(scans, int):
raise TypeError("'scans' must be an integer")
maxima_im = get_maxima_matrix(im, points)
sums = []
numrows = len(maxima_im)
half = int(scans / 2)
for row in range(numrows):
val = 0
for ii in range(scans):
if 0 <= row - half + ii < numrows:
val += maxima_im[row - half + ii].sum()
sums.append(val)
tic = IonChromatogram(numpy.array(sums), im.time_list)
return tic
def __calc_tic(self):
"""
Calculate the total ion chromatogram
:return: Total ion chromatogram
:rtype: pyms.IonChromatogram.IonChromatogram
:author: Qiao Wang
:author: Andrew Isaac
:author: Vladimir Likic
"""
intensities = []
for scan in self._scan_list:
intensities.append(sum(scan.intensity_list))
ia = numpy.array(intensities)
rt = copy.deepcopy(self._time_list)
tic = IonChromatogram(ia, rt)
self._tic = tic
def get_ic_at_index(self, ix: int) -> IonChromatogram:
"""
Returns the ion chromatogram at the specified index.
:param ix: Index of an ion chromatogram in the intensity data matrix.
:return: Ion chromatogram at given index.
:authors: Qiao Wang, Andrew Isaac, Vladimir Likic
"""
if not isinstance(ix, int):
raise TypeError("'ix' must be an integer")
ia = [intensities[ix] for intensities in self._intensity_array]
ic_ia = numpy.array(ia)
mass = self.get_mass_at_index(ix)
rt = self._time_list[:]
return IonChromatogram(ic_ia, rt, mass)
def test_errors_mass(self, value, tic):
with pytest.raises(TypeError):
IonChromatogram(tic.intensity_array, tic.time_list, mass=value)
def test_errors_intensity_list(self, value, tic):
with pytest.raises(TypeError):
IonChromatogram(value, tic.time_list)