def tophat(ic, struct=None):
"""
Top-hat baseline correction on Ion Chromatogram
:param ic: The input ion chromatogram
:type ic: pyms.IonChromatogram.IonChromatogram
:param struct: Top-hat structural element as time string
:type struct: int or str or NoneType, optional
:return: Top-hat corrected ion chromatogram
:rtype: pyms.IonChromatogram.IonChromatogram
:author: Woon Wai Keen
:author: Vladimir Likic
:author: Dominic Davis-Foster (type assertions)
"""
if not isinstance(ic, IonChromatogram):
raise TypeError("'ic' must be an IonChromatogram object")
ia = copy.deepcopy(ic.intensity_array)
if struct:
struct_pts = ic_window_points(ic, struct)
else:
struct_pts = int(round(ia.size * _STRUCT_ELM_FRAC))
# print(" -> Top-hat: structural element is %d point(s)" % ( struct_pts ))
str_el = numpy.repeat([1], struct_pts)
ia = ndimage.white_tophat(ia, footprint=str_el)
ic_bc = copy.deepcopy(ic)
ic_bc.intensity_array = ia
return ic_bc
def tophat(ic: IonChromatogram, struct: Union[int, str, None] = None):
"""
Top-hat baseline correction on Ion Chromatogram.
:param ic: The input ion chromatogram.
:param struct: Top-hat structural element as time string.
The structural element needs to be larger than the features one
wants to retain in the spectrum after the top-hat transform.
:return: Top-hat corrected ion chromatogram.
:authors: Woon Wai Keen, Vladimir Likic, Dominic Davis-Foster (type assertions)
"""
if not isinstance(ic, IonChromatogram):
raise TypeError("'ic' must be an IonChromatogram object")
ia = copy.deepcopy(ic.intensity_array)
if struct:
struct_pts = ic_window_points(ic, struct)
else:
struct_pts = int(round(ia.size * _STRUCT_ELM_FRAC))
# print(f" -> Top-hat: structural element is {struct_pts:d} point(s)")
str_el = numpy.repeat([1], struct_pts)
ia = ndimage.white_tophat(ia, footprint=str_el)
ic_bc = copy.deepcopy(ic)
ic_bc.intensity_array = ia
return ic_bc
def savitzky_golay(ic: IonChromatogram,
window: Union[int, str] = __DEFAULT_WINDOW,
degree=__DEFAULT_POLYNOMIAL_DEGREE) -> IonChromatogram:
"""
Applies Savitzky-Golay filter on ion chromatogram
:param ic: The input ion chromatogram
:type ic: pyms.IonChromatogram.IonChromatogram
:param window: 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: int or str, optional
:param degree: degree of the fitting polynomial for the Savitzky-Golay filter
:type degree: int, optional
:return: Smoothed ion chromatogram
:rtype: pyms.IonChromatogram.IonChromatogram
:author: Uwe Schmitt
:author: Vladimir Likic
:author: Dominic Davis-Foster
"""
if not isinstance(ic, IonChromatogram):
raise TypeError("'ic' must be an IonChromatogram object")
if not isinstance(window, (int, str)):
raise TypeError("'window' must be either an int or a string")
if not isinstance(degree, int):
raise TypeError("'degree' must be an integer")
ia = ic.intensity_array
wing_length = ic_window_points(ic, window, half_window=True)
# print(" -> Applying Savitzky-Golay filter")
# print(" Window width (points): %d" % ( 2*wing_length+1 ))
# print(" Polynomial degree: %d" % ( degree ))
coeff = __calc_coeff(wing_length, degree)
ia_denoise = __smooth(ia, coeff)
ic_denoise = copy.deepcopy(ic)
ic_denoise.intensity_array = ia_denoise
return ic_denoise
def window_smooth(ic: IonChromatogram,
window: Union[int, str] = __DEFAULT_WINDOW,
use_median: bool = False) -> IonChromatogram:
"""
Applies window smoothing on ion chromatogram
:param ic: The input ion chromatogram
:type ic: pyms.IonChromatogram.IonChromatogram
:param window: 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: int or str, optional
:param use_median: An indicator whether the mean or median window smoothing
to be used
:type use_median: bool, optional
:return: Smoothed ion chromatogram
:rtype: pyms.IonChromatogram.IonChromatogram
:author: Vladimir Likic
:author: Dominic Davis-Foster (type assertions)
"""
if not isinstance(ic, IonChromatogram):
raise TypeError("'ic' must be an IonChromatogram object")
if not isinstance(window, (int, str)):
raise TypeError("'window' must be a int or string")
if not isinstance(use_median, bool):
raise TypeError("'median' must be a Boolean")
ia = ic.intensity_array
wing_length = ic_window_points(ic, window, half_window=True)
if use_median:
ia_denoise = __median_window(ia, wing_length)
else:
ia_denoise = __mean_window(ia, wing_length)
ic_denoise = copy.deepcopy(ic)
ic_denoise.intensity_array = ia_denoise
return ic_denoise
def savitzky_golay(ic, window=__DEFAULT_WINDOW, \
degree=__DEFAULT_POLYNOMIAL_DEGREE):
"""
@summary: Applies Savitzky-Golay filter on ion chromatogram
@param ic: The input ion chromatogram
@type ic: pyms.GCMS.Class.IonChromatogram
@param window: 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: IntType or StringType
@param degree: degree of the fitting polynomial for the Savitzky-Golay
filter
@type degree: IntType
@return: Smoothed ion chromatogram
@rtype: pyms.GCMS.Class.IonChromatogram
@author: Uwe Schmitt
@author: Vladimir Likic
"""
if not is_ionchromatogram(ic):
error("'ic' not an IonChromatogram object")
if not is_int(degree):
error("'degree' not an integer")
ia = ic.get_intensity_array()
wing_length = ic_window_points(ic, window, half_window=True)
#print " -> Applying Savitzky-Golay filter"
#print " Window width (points): %d" % ( 2*wing_length+1 )
#print " Polynomial degree: %d" % ( degree )
coeff = __calc_coeff(wing_length, degree)
ia_denoise = __smooth(ia, coeff)
ic_denoise = copy.deepcopy(ic)
ic_denoise.set_intensity_array(ia_denoise)
return ic_denoise
def window_smooth(ic, window=__DEFAULT_WINDOW, median=False):
"""
@summary: Applies window smoothing on ion chromatogram
@param ic: The input ion chromatogram
@type ic: pyms.GCMS.Class.IonChromatogram
@param window: 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: IntType or StringType
@param median: An indicator whether the mean or median window smoothing
to be used
@type median: Booleantype
@return: Smoothed ion chromatogram
@rtype: pyms.GCMS.Class.IonChromatogram
@author: Vladimir Likic
"""
if not is_ionchromatogram(ic):
error("'ic' not an IonChromatogram object")
ia = ic.get_intensity_array()
wing_length = ic_window_points(ic, window, half_window=True)
if median:
ia_denoise = __median_window(ia, wing_length)
else:
ia_denoise = __mean_window(ia, wing_length)
ic_denoise = copy.deepcopy(ic)
ic_denoise.set_intensity_array(ia_denoise)
return ic_denoise
def window_smooth(ic, window=__DEFAULT_WINDOW, median=False):
"""
@summary: Applies window smoothing on ion chromatogram
@param ic: The input ion chromatogram
@type ic: pyms.GCMS.Class.IonChromatogram
@param window: 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: IntType or StringType
@param median: An indicator whether the mean or median window smoothing
to be used
@type median: Booleantype
@return: Smoothed ion chromatogram
@rtype: pyms.GCMS.Class.IonChromatogram
@author: Vladimir Likic
"""
if not is_ionchromatogram(ic):
error("'ic' not an IonChromatogram object")
ia = ic.get_intensity_array()
wing_length = ic_window_points(ic, window, half_window=True)
if median:
ia_denoise = __median_window(ia, wing_length)
else:
ia_denoise = __mean_window(ia, wing_length)
ic_denoise = copy.deepcopy(ic)
ic_denoise.set_intensity_array(ia_denoise)
return ic_denoise
def tophat(ic, struct=None):
"""
@summary: Top-hat baseline correction on Ion Chromatogram
@param ic: The input ion chromatogram
@type ic: pyms.GCMS.Class.IonChromatogram
@param struct: Top-hat structural element as time string
@type struct: StringType
@return: Top-hat corrected ion chromatogram
@rtype: pyms.IO.Class.IonChromatogram
@author: Woon Wai Keen
@author: Vladimir Likic
"""
if not is_ionchromatogram(ic):
error("'ic' not an IonChromatogram object")
else:
ia = copy.deepcopy(ic.get_intensity_array())
if struct == None:
struct_pts = int(round(ia.size * _STRUCT_ELM_FRAC))
else:
struct_pts = ic_window_points(ic, struct)
# print " -> Top-hat: structural element is %d point(s)" % ( struct_pts )
str_el = numpy.repeat([1], struct_pts)
ia = ndimage.white_tophat(ia, None, str_el)
ic_bc = copy.deepcopy(ic)
ic_bc.set_intensity_array(ia)
return ic_bc
def tophat(ic, struct=None):
"""
@summary: Top-hat baseline correction on Ion Chromatogram
@param ic: The input ion chromatogram
@type ic: pyms.GCMS.Class.IonChromatogram
@param struct: Top-hat structural element as time string
@type struct: StringType
@return: Top-hat corrected ion chromatogram
@rtype: pyms.IO.Class.IonChromatogram
@author: Woon Wai Keen
@author: Vladimir Likic
"""
if not is_ionchromatogram(ic):
error("'ic' not an IonChromatogram object")
else:
ia = copy.deepcopy(ic.get_intensity_array())
if struct == None:
struct_pts = int(round(ia.size * _STRUCT_ELM_FRAC))
else:
struct_pts = ic_window_points(ic,struct)
# print " -> Top-hat: structural element is %d point(s)" % ( struct_pts )
str_el = numpy.repeat([1], struct_pts)
ia = ndimage.white_tophat(ia, None, str_el)
ic_bc = copy.deepcopy(ic)
ic_bc.set_intensity_array(ia)
return ic_bc