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 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 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
