def add_gaussv_noise_ic(ic: IonChromatogram, scale: int, cutoff: int,
prop: float):
"""
Adds noise to an ic. The noise value is drawn from a normal
distribution, the scale of this distribution depends on the
value of the ic at the point where the noise is being added
:param ic: The IonChromatogram
:type ic: pyms.IonChromatogram.IonChromatogram
:param cutoff: The level below which the intensity of the ic at that point
has no effect on the scale of the noise distribution
:type cutoff: int
:param scale: The scale of the normal distribution for ic values below the cutoff
is modified for values above the cutoff
:type scale: int
:param prop: For ic values above the cutoff, the scale is multiplied by the ic
value multiplied by prop
:type prop: float
:author: Sean O'Callaghan
"""
noise = numpy.zeros(len(ic))
i_array = ic.get_intensity_array()
# time_list = ic.get_time_list()
for i in range(len(ic)):
if i_array[i] < cutoff:
noise[i] = numpy.random.normal(0.0, scale, 1)
else:
noise[i] = numpy.random.normal(0.0, scale * i_array[i] * prop, 1)
i_array_with_noise = noise + i_array
ic.set_intensity_array(i_array_with_noise)
def get_maxima_list(ic: IonChromatogram, points: List = 3) -> int:
"""
List of retention time and intensity of local maxima for ion
:param ic: An :class:`~pyms.IonChromatogram.IonChromatogram` object
:type ic: ~pyms.IonChromatogram.IonChromatogram
:param points: Number of scans over which to consider a maxima to be a peak. Default ``3``
:type points: int
:return: A list of retention time and intensity of local maxima for ion
:rtype: list
:author: Andrew Isaac, Dominic Davis-Foster (type assertions)
"""
if not isinstance(ic, IonChromatogram):
raise TypeError("'ic' must be an IonChromatogram object")
if not isinstance(points, int):
raise TypeError("'points' must be an integer")
peak_point = get_maxima_indices(ic.intensity_array, points)
mlist = []
for index in range(len(peak_point)):
rt = ic.get_time_at_index(peak_point[index])
intensity = ic.get_intensity_at_index(peak_point[index])
mlist.append([rt, intensity])
return mlist
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 plot_tic(self, tic: IonChromatogram, minutes: bool = False, **kwargs):
"""
Plots a Total Ion Chromatogram.
:param tic: Total Ion Chromatogram.
:param minutes: Whether to show the time in minutes.
:Other Parameters: :class:`matplotlib.lines.Line2D` properties.
Used to specify properties like a line label (for auto legends),
linewidth, antialiasing, marker face color.
Example::
>>> plot_tic(data.tic, label='TIC', linewidth=2)
See https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.lines.Line2D.html
for the list of possible kwargs
"""
if not isinstance(tic, IonChromatogram) or not tic.is_tic():
raise TypeError("'tic' must be an Ion Chromatogram object representing a total ion chromatogram")
plot = plot_ic(self.ax, tic, minutes, **kwargs)
self.__tic_ic_plots.append(plot)
return plot
def add_gaussc_noise_ic(ic: IonChromatogram, scale: float):
"""
Adds noise drawn from a normal distribution with constant scale to an ion chromatogram
:param ic: The ion Chromatogram
:type ic: pyms.IonChromatogram.IonChromatogram
:param scale: The scale of the normal distribution
:type scale: float
:author: Sean O'Callaghan
"""
noise = numpy.random.normal(0.0, scale, (len(ic)))
i_array_with_noise = ic.get_intensity_array() + noise
ic.set_intensity_array(i_array_with_noise)
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 get_maxima_list_reduced(ic: IonChromatogram,
mp_rt: float,
points: int = 13,
window: int = 3) -> List:
"""
List of retention time and intensity of local maxima for ion.
Only peaks around a specific retention time are recorded
Created for use with gap filling algorithm.
:param ic: An :class:`~pyms.IonChromatogram.IonChromatogram` object
:type ic: ~pyms.IonChromatogram.IonChromatogram
:param mp_rt: The retention time of the missing peak
:type mp_rt: float
:param points: Number of scans over which to consider a maxima to be a peak. Default ``13``
:type points: int, optional
:param window: The window around the ``mp_rt`` where peaks should be recorded. Default ``3``
:type window: int, optional
:return: A list of retention time and intensity of local maxima for ion
:rtype: list
:author: Andrew Isaac, Dominic Davis-Foster (type assertions)
"""
if not isinstance(ic, IonChromatogram):
raise TypeError("'ic' must be an IonChromatogram object")
if not isinstance(mp_rt, Number):
raise TypeError("'mp_rt' must be an integer")
# if not isinstance(scans, int):
# raise TypeError("'scans' must be an integer")
peak_point = get_maxima_indices(ic.intensity_array, points)
maxima_list = []
for index in range(len(peak_point)):
rt = ic.get_time_at_index(peak_point[index])
if (rt > float(mp_rt) - window) and (rt < float(mp_rt) + window):
intensity = ic.get_intensity_at_index(peak_point[index])
maxima_list.append([rt, intensity])
else:
pass
return maxima_list
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 window_sele_points(ic: IonChromatogram,
window_sele: Union[int, str],
half_window: bool = False) -> int:
"""
Converts window selection parameter into points based
on the time step in an ion chromatogram
:param ic: ion chromatogram object relevant for the conversion
:type ic: pyms.IonChromatogram.IonChromatogram
:param window_sele: The window selection parameter. This can be
an integer or time string. If integer, taken as the number
of points. If a string, must of the form "<NUMBER>s" or
"<NUMBER>m", specifying a time in seconds or minutes,
respectively
:type window_sele: int or str
:param half_window: Specifies whether to return half-window
:type half_window: bool
:return: The number of points in the window
:rtype: int
:author: Vladimir Likic
"""
if not isinstance(window_sele, int) and not isinstance(window_sele, str):
raise TypeError("'window' must be an integer or a string")
if isinstance(window_sele, int):
if half_window:
if window_sele % 2 == 0:
raise TypeError("window must be an odd number of points")
else:
points = int(math.floor(window_sele * 0.5))
else:
points = window_sele
else:
time = time_str_secs(window_sele)
time_step = ic.get_time_step()
if half_window:
time = time * 0.5
points = int(math.floor(time / time_step))
if half_window:
if points < 1:
raise ValueError(f"window too small (half window={points:d})")
else:
if points < 2:
raise ValueError(f"window too small (window={points:d})")
return points
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 get_maxima_list_reduced(
ic: IonChromatogram,
mp_rt: float,
points: int = 13,
window: int = 3,
) -> List[Tuple[float, float]]:
"""
List of retention time and intensity of local maxima for ion.
| Only peaks around a specific retention time are recorded.
| Created for use with gap filling algorithm.
:param ic:
:param mp_rt: The retention time of the missing peak
:param points: Number of scans over which to consider a maxima to be a peak.
:param window: The window around ``mp_rt`` where peaks should be recorded.
:return: A list of 2-element tuple containing the retention time and
intensity of local maxima for each ion.
:author: Andrew Isaac, Dominic Davis-Foster (type assertions)
"""
if not isinstance(ic, IonChromatogram):
raise TypeError("'ic' must be an IonChromatogram object")
if not is_number(mp_rt):
raise TypeError("'mp_rt' must be a number")
peak_point = get_maxima_indices(ic.intensity_array, points)
maxima_list = []
for index in range(len(peak_point)):
rt = ic.get_time_at_index(peak_point[index])
if (rt > float(mp_rt) - window) and (rt < float(mp_rt) + window):
intensity = ic.get_intensity_at_index(peak_point[index])
maxima_list.append((rt, intensity))
return maxima_list
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_intensity_list(self, value, tic):
with pytest.raises(TypeError):
IonChromatogram(value, tic.time_list)
def test_errors_mass(self, value, tic):
with pytest.raises(TypeError):
IonChromatogram(tic.intensity_array, tic.time_list, mass=value)
