Example #1
0
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
Example #2
0
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
Example #3
0
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
Example #4
0
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
Example #5
0
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
Example #6
0
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
Example #7
0
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
Example #8
0
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
Example #9
0
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