Esempio n. 1
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    def __init__(self, time_list, scan_list):

        """
        @summary: Initialize the GC-MS data

        @param time_list: List of scan retention times
        @type time_list: ListType
        @param scan_list: List of Scan objects
        @type scan_list: ListType

        @author: Qiao Wang
        @author: Andrew Isaac
        @author: Vladimir Likic
        """

        if not is_list(time_list) or not is_number(time_list[0]):
            error("'time_list' must be a list of numbers")

        if not is_list(scan_list) or not isinstance(scan_list[0], Scan):
            error("'scan_list' must be a list of Scan objects")

        self.__set_time(time_list)
        self.__scan_list = scan_list
        self.__set_min_max_mass()
        self.__calc_tic()
Esempio n. 2
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    def __init__(self, mass_list, intensity_list):

        """
        @summary: Initialise the MassSpectrum

        @param mass_list: List of binned masses
        @type mass_list: ListType
        @param intensity_list: List of binned intensities
        @type intensity_list: ListType

        @author: Andrew Isaac
        @author: Qiao Wang
        @author: Vladimir Likic
        """

        if not is_list(mass_list) or not is_number(mass_list[0]):
            error("'mass_list' must be a list of numbers")
        if not is_list(intensity_list) or \
           not is_number(intensity_list[0]):
            error("'intensity_list' must be a list of numbers")
        if not len(mass_list) == len(intensity_list):
            error("'mass_list' is not the same size as 'intensity_list'")

        #TODO: should these be public, or accessed through methods???
        self.mass_list = mass_list
        self.mass_spec = intensity_list
Esempio n. 3
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def rmsd(list1, list2):

    """
    @summary: Calculates RMSD for the 2 lists

    @param list1: First data set
    @type list1: ListType, TupleType, or numpy.core.ndarray 
    @param list2: Second data set
    @type list2: ListType, TupleType, or numpy.core.ndarray 
    @return: RMSD value
    @rtype: FloatType

    @author: Qiao Wang
    @author: Andrew Isaac
    @author: Vladimir Likic
    """

    if not is_list(list1):
        error("argument neither list nor array")

    if not is_list(list2):
        error("argument neither list nor array")

    sum = 0.0
    for i in range(len(list1)):
        sum = sum + (list1[i] - list2[i]) ** 2
    rmsd = math.sqrt(sum / len(list1))
    return rmsd
Esempio n. 4
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    def __init__(self, time_list, scan_list):

        """
        @summary: Initialize the GC-MS data

        @param time_list: List of scan retention times
        @type time_list: ListType
        @param scan_list: List of Scan objects
        @type scan_list: ListType

        @author: Qiao Wang
        @author: Andrew Isaac
        @author: Vladimir Likic
        """

        if not is_list(time_list) or not is_number(time_list[0]):
            error("'time_list' must be a list of numbers")

        if not is_list(scan_list) or not isinstance(scan_list[0], Scan):
            error("'scan_list' must be a list of Scan objects")

        self.__set_time(time_list)
        self.__scan_list = scan_list
        self.__set_min_max_mass()
        self.__calc_tic()
Esempio n. 5
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    def __init__(self, mass_list, intensity_list):

        """
        @summary: Initialize the Scan data

        @param mass_list: mass values
        @type mass_list: ListType

        @param intensity_list: intensity values
        @type intensity_list: ListType

        @author: Qiao Wang
        @author: Andrew Isaac
        @author: Vladimir Likic
        """

        if not is_list(mass_list) or not is_number(mass_list[0]):
            error("'mass_list' must be a list of numbers")
        if not is_list(intensity_list) or \
           not is_number(intensity_list[0]):
            error("'intensity_list' must be a list of numbers")

        self.__mass_list = mass_list
        self.__intensity_list = intensity_list
        self.__min_mass = min(mass_list)
        self.__max_mass = max(mass_list)
Esempio n. 6
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    def __init__(self, mass_list, intensity_list):

        """
        @summary: Initialize the Scan data

        @param mass_list: mass values
        @type mass_list: ListType

        @param intensity_list: intensity values
        @type intensity_list: ListType

        @author: Qiao Wang
        @author: Andrew Isaac
        @author: Vladimir Likic
        """

        if not is_list(mass_list) or not is_number(mass_list[0]):
            error("'mass_list' must be a list of numbers")
        if not is_list(intensity_list) or \
           not is_number(intensity_list[0]):
            error("'intensity_list' must be a list of numbers")

        self.__mass_list = mass_list
        self.__intensity_list = intensity_list
        self.__min_mass = min(mass_list)
        self.__max_mass = max(mass_list)
Esempio n. 7
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    def __init__(self, mass_list, intensity_list):

        """
        @summary: Initialise the MassSpectrum

        @param mass_list: List of binned masses
        @type mass_list: ListType
        @param intensity_list: List of binned intensities
        @type intensity_list: ListType

        @author: Andrew Isaac
        @author: Qiao Wang
        @author: Vladimir Likic
        """

        if not is_list(mass_list) or not is_number(mass_list[0]):
            error("'mass_list' must be a list of numbers")
        if not is_list(intensity_list) or \
           not is_number(intensity_list[0]):
            error("'intensity_list' must be a list of numbers")
        if not len(mass_list) == len(intensity_list):
            error("'mass_list' is not the same size as 'intensity_list'")

        #TODO: should these be public, or accessed through methods???
        self.mass_list = mass_list
        self.mass_spec = intensity_list
Esempio n. 8
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File: IO.py Progetto: DongElkan/pyms
def load_peaks(file_name):

    """
    @summary: Loads the peak_list stored with 'store_peaks'

    @param file_name: File name of peak list
    @type file_name: StringType

    @return: The list of Peak objects
    @rtype: ListType

    @author: Andrew Isaac
    """

    if not is_str(file_name):
        error("'file_name' not a string")

    fp = open(file_name,'r')
    peak_list = cPickle.load(fp)
    fp.close()

    if not is_list(peak_list):
        error("'file_name' is not a List")
    if not len(peak_list) > 0 and not isinstance(peak_list[0], Peak):
        error("'peak_list' must be a list of Peak objects")

    return peak_list
Esempio n. 9
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def load_peaks(file_name):
    """
    @summary: Loads the peak_list stored with 'store_peaks'

    @param file_name: File name of peak list
    @type file_name: StringType

    @return: The list of Peak objects
    @rtype: ListType

    @author: Andrew Isaac
    """

    if not is_str(file_name):
        error("'file_name' not a string")

    fp = open(file_name, 'r')
    peak_list = cPickle.load(fp)
    fp.close()

    if not is_list(peak_list):
        error("'file_name' is not a List")
    if not len(peak_list) > 0 and not isinstance(peak_list[0], Peak):
        error("'peak_list' must be a list of Peak objects")

    return peak_list
Esempio n. 10
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def exprl2alignment(exprl):

    """
    @summary: Converts experiments into alignments

    @param exprl: The list of experiments to be converted into an alignment
        objects
    @type exprl: ListType

    @author: Vladimir Likic
    """

    if not is_list(exprl):
        error("the argument is not a list")

    algts = []

    for item in exprl:
        if not isinstance(item, Experiment):
            error("list items must be 'Experiment' instances")
        else:
            algt = Class.Alignment(item)
        algts.append(algt)

    return algts
Esempio n. 11
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def is_peak_list(peaks):

    """
    @summary: Returns True if 'peaks' is a valid peak list, False
    otherwise

    @param peaks: A list of peak objects
    @type peaks: ListType

    @return: A boolean indicator
    @rtype: BooleanType

    @author: Vladimir Likic
    """

    flag = True

    if not is_list(peaks):
        flag = False
    else:
        for item in peaks:
            if not isinstance(item, Peak):
                flag = False

    return flag
Esempio n. 12
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    def __init__(self, ia, time_list, mass=None):

        """
        @param ia: Ion chromatogram intensity values
        @type ia: numpy.array
        @param time_list: A list of ion chromatogram retention times
        @type time_list: ListType
        @param mass: Mass of ion chromatogram (Null if TIC)
        @type mass: IntType

        @author: Lewis Lee
        @author: Vladimir Likic
        @author: Vladimir Likic
        """

        if not isinstance(ia, numpy.ndarray):
            error("'ia' must be a numpy array")

        if not is_list(time_list) or not is_number(time_list[0]):
            error("'time_list' must be a list of numbers")

        if len(ia) != len(time_list):
            error("Intensity array and time list differ in length")

        self.__ia = ia
        self.__time_list = time_list
        self.__mass = mass
        self.__time_step = self.__calc_time_step(time_list)
        self.__min_rt = min(time_list)
        self.__max_rt = max(time_list)
Esempio n. 13
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def MAD(v):

    """
    @summary: median absolute deviation

    @param v: A list or array
    @type v: ListType, TupleType, or numpy.core.ndarray

    @return: median absolute deviation
    @rtype: FloatType

    @author: Vladimir Likic
    """

    if not is_list(v):
        error("argument neither list nor array")

    m = median(v)
    m_list = []

    for xi in v:
        d = math.fabs(xi - m)
        m_list.append(d)

    mad = median(m_list)/0.6745

    return mad
Esempio n. 14
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def median(v):

    """
    @summary: Returns a median of a list or numpy array

    @param v: Input list or array
    @type v: ListType or numpy.core.ndarray
    @return: The median of the input list
    @rtype: FloatType

    @author: Vladimir Likic
    """

    if not is_list(v):
        error("argument neither list nor array")

    local_data = copy.deepcopy(v)
    local_data.sort()
    N = len(local_data)

    if (N % 2) == 0:
        # even number of points
        K = N/2 - 1 
        median = (local_data[K] + local_data[K+1])/2.0
    else:
	    # odd number of points
        K = (N - 1)/2 - 1
        median = local_data[K+1]

    return median
Esempio n. 15
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def std(v):

    """
    @summary: Calculates standard deviation

    @param v: A list or array
    @type v: ListType, TupleType, or numpy.core.ndarray

    @return: Mean
    @rtype: FloatType

    @author: Vladimir Likic
    """

    if not is_list(v):
        error("argument neither list nor array")

    v_mean = mean(v)

    s = 0.0 
    for e in v:
        d = e - v_mean
        s = s + d*d
    s_mean = s/float(len(v)-1)
    v_std = math.sqrt(s_mean)

    return v_std
Esempio n. 16
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def amin(v):

    """
    @summary: Finds the minimum element in a list or array

    @param v: A list or array
    @type v: ListType, TupleType, or numpy.core.ndarray

    @return: Tuple (maxi, maxv), where maxv is the minimum 
        element in the list and maxi is its index
    @rtype: TupleType

    @author: Vladimir Likic
    """

    if not is_list(v):
        error("argument neither list nor array")

    minv = max(v) # built-in max() function
    mini = None

    for ii in range(len(v)):
        if v[ii] < minv:
            minv = v[ii]
            mini = ii

    if mini == None:
        error("finding maximum failed")

    return mini, minv
Esempio n. 17
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    def __init__(self, ia, time_list, mass=None):

        """
        @param ia: Ion chromatogram intensity values
        @type ia: numpy.array
        @param time_list: A list of ion chromatogram retention times
        @type time_list: ListType
        @param mass: Mass of ion chromatogram (Null if TIC)
        @type mass: IntType

        @author: Lewis Lee
        @author: Vladimir Likic
        @author: Vladimir Likic
        """

        if not isinstance(ia, numpy.ndarray):
            error("'ia' must be a numpy array")

        if not is_list(time_list) or not is_number(time_list[0]):
            error("'time_list' must be a list of numbers")

        if len(ia) != len(time_list):
            error("Intensity array and time list differ in length")

        self.__ia = ia
        self.__time_list = time_list
        self.__mass = mass
        self.__time_step = self.__calc_time_step(time_list)
        self.__min_rt = min(time_list)
        self.__max_rt = max(time_list)
Esempio n. 18
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def exprl2alignment(exprl):

    """
    @summary: Converts experiments into alignments

    @param exprl: The list of experiments to be converted into an alignment
        objects
    @type exprl: ListType

    @author: Vladimir Likic
    """

    if not is_list(exprl):
        error("the argument is not a list")

    algts = []

    for item in exprl:
        if not isinstance(item, Experiment):
            error("list items must be 'Experiment' instances")
        else:
            algt = Class.Alignment(item)
        algts.append(algt)

    return algts
Esempio n. 19
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def median_bounds(im, peak, shared=True):

    """
    @Summary: Calculates the median of the left and right bounds found
        for each apexing peak mass

    @param im: The originating IntensityMatrix object
    @type im: pyms.GCMS.Class.IntensityMatrix
    @param peak: The Peak object
    @type peak: pyms.Peak.Class.Peak
    @param shared: Include shared ions shared with neighbouring peak
    @type shared: BooleanType

    @return: median left and right boundary offset in points
    @rtype: TupleType

    @author: Andrew Isaac
    """

    mat = im.get_matrix_list()
    ms = peak.get_mass_spectrum()
    rt = peak.get_rt()
    apex = im.get_index_at_time(rt)
    # check if RT based index is simmilar to stored index
    tmp = peak.get_pt_bounds()
    if is_list(tmp) and apex-1 < tmp[1] and tmp[1] < apex+1:
        apex = tmp[1]

    # get peak masses with non-zero intensity
    mass_ii = [ ii for ii in xrange(len(ms.mass_list)) \
        if ms.mass_spec[ii] > 0 ]

    # get stats on boundaries
    left_list = []
    right_list = []
    for ii in mass_ii:
        # get ion chromatogram as list
        ia = [ mat[scan][ii] for scan in xrange(len(mat)) ]
        area, left, right, l_share, r_share = ion_area(ia, apex)
        if shared or not l_share:
            left_list.append(left)
        if shared or not r_share:
            right_list.append(right)

    # return medians
    # NB if shared=True, lists maybe empty
    l_med = 0
    r_med = 0
    if len(left_list) > 0:
        l_med = median(left_list)
    if len(right_list) > 0:
        r_med = median(right_list)

    return l_med, r_med
Esempio n. 20
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def median_bounds(im, peak, shared=True):
    """
    @Summary: Calculates the median of the left and right bounds found
        for each apexing peak mass

    @param im: The originating IntensityMatrix object
    @type im: pyms.GCMS.Class.IntensityMatrix
    @param peak: The Peak object
    @type peak: pyms.Peak.Class.Peak
    @param shared: Include shared ions shared with neighbouring peak
    @type shared: BooleanType

    @return: median left and right boundary offset in points
    @rtype: TupleType

    @author: Andrew Isaac
    """

    mat = im.get_matrix_list()
    ms = peak.get_mass_spectrum()
    rt = peak.get_rt()
    apex = im.get_index_at_time(rt)
    # check if RT based index is simmilar to stored index
    tmp = peak.get_pt_bounds()
    if is_list(tmp) and apex - 1 < tmp[1] and tmp[1] < apex + 1:
        apex = tmp[1]

    # get peak masses with non-zero intensity
    mass_ii = [ ii for ii in xrange(len(ms.mass_list)) \
        if ms.mass_spec[ii] > 0 ]

    # get stats on boundaries
    left_list = []
    right_list = []
    for ii in mass_ii:
        # get ion chromatogram as list
        ia = [mat[scan][ii] for scan in xrange(len(mat))]
        area, left, right, l_share, r_share = ion_area(ia, apex)
        if shared or not l_share:
            left_list.append(left)
        if shared or not r_share:
            right_list.append(right)

    # return medians
    # NB if shared=True, lists maybe empty
    l_med = 0
    r_med = 0
    if len(left_list) > 0:
        l_med = median(left_list)
    if len(right_list) > 0:
        r_med = median(right_list)

    return l_med, r_med
Esempio n. 21
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def get_maxima_indices(ion_intensities, points=3):

    """
    @summary: Find local maxima.

    @param ion_intensities: A list of intensities for a single ion
    @type ion_intensities: ListType
    @param points: Peak if maxima over 'points' number of scans
    @type points: IntType

    @return: A list of scan indices
    @rtype: ListType

    @author: Andrew Isaac
    """

    if not is_list(ion_intensities) or not is_number(ion_intensities[0]):
        error("'ion_intensities' must be a List of numbers")

    # find peak inflection points
    # use a 'points' point window
    # for a plateau after a rise, need to check if it is the left edge of
    # a peak
    peak_point = []
    edge = -1
    points = int(points)
    half = int(points/2)
    points = 2*half+1  # ensure odd number of points
    for index in range(len(ion_intensities)-points+1):
        left = ion_intensities[index:index+half]
        mid = ion_intensities[index+half]
        right = ion_intensities[index+half+1:index+points]
        # max in middle
        if mid > max(left) and mid > max(right):
            peak_point.append(index+half)
            edge = -1  # ignore previous rising edge
        # flat from rise (left of peak?)
        if mid > max(left) and mid == max(right):
            edge = index+half  # ignore previous rising edge, update latest
        # fall from flat
        if mid == max(left) and mid > max(right):
            if edge > -1:
                centre = int((edge+index+half)/2)  # mid point
                peak_point.append(centre)
            edge = -1

    return peak_point
Esempio n. 22
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def get_maxima_indices(ion_intensities, points=3):

    """
    @summary: Find local maxima.

    @param ion_intensities: A list of intensities for a single ion
    @type ion_intensities: ListType
    @param points: Peak if maxima over 'points' number of scans
    @type points: IntType

    @return: A list of scan indices
    @rtype: ListType

    @author: Andrew Isaac
    """

    if not is_list(ion_intensities) or not is_number(ion_intensities[0]):
        error("'ion_intensities' must be a List of numbers")

    # find peak inflection points
    # use a 'points' point window
    # for a plateau after a rise, need to check if it is the left edge of
    # a peak
    peak_point = []
    edge = -1
    points = int(points)
    half = int(points/2)
    points = 2*half+1  # ensure odd number of points
    for index in range(len(ion_intensities)-points+1):
        left = ion_intensities[index:index+half]
        mid = ion_intensities[index+half]
        right = ion_intensities[index+half+1:index+points]
        # max in middle
        if mid > max(left) and mid > max(right):
            peak_point.append(index+half)
            edge = -1  # ignore previous rising edge
        # flat from rise (left of peak?)
        if mid > max(left) and mid == max(right):
            edge = index+half  # ignore previous rising edge, update latest
        # fall from flat
        if mid == max(left) and mid > max(right):
            if edge > -1:
                centre = int((edge+index+half)/2)  # mid point
                peak_point.append(centre)
            edge = -1

    return peak_point
Esempio n. 23
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def sele_peaks_by_rt(peaks, rt_range):

    """
    @summary: Selects peaks from a retention time range

    @param peaks: A list of peak objects
    @type peaks: ListType
    @param rt_range: A list of two time strings, specifying lower and
           upper retention times
    @type rt_range: ListType
    @return: A list of peak objects
    @rtype: ListType
    """

    if not is_peak_list(peaks):
        error("'peaks' not a peak list")

    if not is_list(rt_range):
        error("'rt_range' not a list")
    else:
        if len(rt_range) != 2:
            error("'rt_range' must have exactly two elements")

        if not is_str(rt_range[0]) or not is_str(rt_range[1]):
            error("lower/upper retention time limits must be strings")

    rt_lo = time_str_secs(rt_range[0])
    rt_hi = time_str_secs(rt_range[1])

    if not rt_lo < rt_hi:
        error("lower retention time limit must be less than upper")

    peaks_sele = []

    for peak in peaks:
        rt = peak.get_rt()
        if rt > rt_lo and rt < rt_hi:
            peaks_sele.append(peak)

    # print "%d peaks selected" % (len(peaks_sele))

    return peaks_sele
Esempio n. 24
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def mean(v):

    """
    @summary: Calculates the mean

    @param v: A list or array
    @type v: ListType, TupleType, or numpy.core.ndarray

    @return: Mean
    @rtype: FloatType

    @author: Vladimir Likic
    """

    if not is_list(v):
        error("argument neither list nor array")

    s = 0.0
    for e in v:
        s = s + e 
    s_mean = s/float(len(v))

    return s_mean
Esempio n. 25
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    def set_pt_bounds(self, pt_bounds):
        """
        @summary: Sets peak boundaries in points

        @param pt_bounds: A list containing left, apex, and right
            peak boundaries in points, left and right are offsets
        @type pt_bounds: ListType

        @return: none
        @rtype: NoneType
        """

        if not is_list(pt_bounds):
            error("'pt_bounds' must be a list")

        if not len(pt_bounds) == 3:
            error("'pt_bounds' must have exactly 3 elements")
        else:
            for item in pt_bounds:
                if not is_int(item):
                    error("'pt_bounds' element not an integer")

        self.__pt_bounds = pt_bounds
Esempio n. 26
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    def set_pt_bounds(self, pt_bounds):

        """
        @summary: Sets peak boundaries in points

        @param pt_bounds: A list containing left, apex, and right
            peak boundaries in points, left and right are offsets
        @type pt_bounds: ListType

        @return: none
        @rtype: NoneType
        """

        if not is_list(pt_bounds):
            error("'pt_bounds' must be a list")

        if not len(pt_bounds) == 3:
            error("'pt_bounds' must have exactly 3 elements")
        else:
            for item in pt_bounds:
                if not is_int(item):
                    error("'pt_bounds' element not an integer")

        self.__pt_bounds = pt_bounds
Esempio n. 27
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    def __init__(self, time_list, mass_list, intensity_matrix):

        """
        @summary: Initialize the IntensityMatrix data

        @param time_list: Retention time values
        @type time_list: ListType

        @param mass_list: Binned mass values
        @type mass_list: ListType

        @param intensity_matrix: Binned intensity values per scan
        @type intensity_matrix: ListType

        @author: Andrew Isaac
        """

        # sanity check
        if not is_list(time_list) or not is_number(time_list[0]):
            error("'time_list' must be a list of numbers")
        if not is_list(mass_list) or not is_number(mass_list[0]):
            error("'mass_list' must be a list of numbers")
        if not is_list(intensity_matrix) or \
           not is_list(intensity_matrix[0]) or \
           not is_number(intensity_matrix[0][0]):
            error("'intensity_matrix' must be a list, of a list, of numbers")
        if not len(time_list) == len(intensity_matrix):
            error("'time_list' is not the same length as 'intensity_matrix'")
        if not len(mass_list) == len(intensity_matrix[0]):
            error("'mass_list' is not the same size as 'intensity_matrix'"
                " width")

        self.__time_list = time_list
        self.__mass_list = mass_list
        self.__intensity_matrix = intensity_matrix

        self.__min_mass = min(mass_list)
        self.__max_mass = max(mass_list)

        # Direct access for speed (DANGEROUS)
        self.intensity_matrix = self.__intensity_matrix

        # Try to include parallelism.
        try:
            from mpi4py import MPI
            comm = MPI.COMM_WORLD
            num_ranks = comm.Get_size()
            rank = comm.Get_rank()
            M, N = len(intensity_matrix), len(intensity_matrix[0])
            lrr = (rank*M/num_ranks, (rank + 1)*M/num_ranks)
            lcr = (rank*N/num_ranks, (rank + 1)*N/num_ranks)
            m, n = (lrr[1] - lrr[0], lcr[1] - lcr[0])
            self.comm = comm
            self.num_ranks = num_ranks
            self.rank = rank
            self.M = M
            self.N = N
            self.local_row_range = lrr
            self.local_col_range = lcr
            self.m = m
            self.n = n

        # If we can't import mpi4py then continue in serial.
        except:
            pass
Esempio n. 28
0
def save_data(file_name,
              data,
              format_str="%.6f",
              prepend="",
              sep=" ",
              compressed=False):
    """
    @summary: Saves a list of numbers or a list of lists of numbers
    to a file with specific formatting

    @param file_name: Name of a file
    @type: StringType
    @param data: A list of numbers, or a list of lists
    @type: ListType
    @param format_str: A format string for individual entries
    @type: StringType
    @param prepend: A string, printed before each row
    @type: StringType
    @param sep: A string, printed after each number
    @type: StringType
    @param compressed: A boolean. If True, the output will be gzipped
    @type: BooleanType

    @return: none
    @rtype: NoneType

    @author: Vladimir Likic
    """

    if not is_str(file_name):
        error("'file_name' is not a string")

    if not is_list(data):
        error("'data' is not a list")

    if not is_str(prepend):
        error("'prepend' is not a string")

    if not is_str(sep):
        error("'sep' is not a string")

    fp = open_for_writing(file_name)

    # decide whether data is a vector or matrix
    if is_number(data[0]):
        for item in data:
            if not is_number(item):
                error("not all elements of the list are numbers")
        data_is_matrix = 0
    else:
        for item in data:
            if not is_list(item):
                error("not all elements of the list are lists")
        data_is_matrix = 1

    if data_is_matrix:
        for ii in range(len(data)):
            fp.write(prepend)
            for jj in range(len(data[ii])):
                if is_number(data[ii][jj]):
                    fp.write(format_str % (data[ii][jj]))
                    if (jj < (len(data[ii]) - 1)): fp.write(sep)
                else:
                    error("datum not a number")
            fp.write("\n")
    else:
        for ii in range(len(data)):
            fp.write(prepend)
            fp.write(format_str % (data[ii]))
            fp.write("\n")

    close_for_writing(fp)

    if compressed:
        status = os.system('gzip %s' % (file_name))
        if status != 0:
            error("gzip compress failed")
Esempio n. 29
0
    def __init__(self, time_list, mass_list, intensity_matrix):

        """
        @summary: Initialize the IntensityMatrix data

        @param time_list: Retention time values
        @type time_list: ListType

        @param mass_list: Binned mass values
        @type mass_list: ListType

        @param intensity_matrix: Binned intensity values per scan
        @type intensity_matrix: ListType

        @author: Andrew Isaac
        """

        # sanity check
        if not is_list(time_list) or not is_number(time_list[0]):
            error("'time_list' must be a list of numbers")
        if not is_list(mass_list) or not is_number(mass_list[0]):
            error("'mass_list' must be a list of numbers")
        if not is_list(intensity_matrix) or \
           not is_list(intensity_matrix[0]) or \
           not is_number(intensity_matrix[0][0]):
            error("'intensity_matrix' must be a list, of a list, of numbers")
        if not len(time_list) == len(intensity_matrix):
            error("'time_list' is not the same length as 'intensity_matrix'")
        if not len(mass_list) == len(intensity_matrix[0]):
            error("'mass_list' is not the same size as 'intensity_matrix'"
                " width")

        self.__time_list = time_list
        self.__mass_list = mass_list
        self.__intensity_matrix = intensity_matrix

        self.__min_mass = min(mass_list)
        self.__max_mass = max(mass_list)

        # Direct access for speed (DANGEROUS)
        self.intensity_matrix = self.__intensity_matrix

        # Try to include parallelism.
        try:
            from mpi4py import MPI
            comm = MPI.COMM_WORLD
            num_ranks = comm.Get_size()
            rank = comm.Get_rank()
            M, N = len(intensity_matrix), len(intensity_matrix[0])
            lrr = (rank*M/num_ranks, (rank + 1)*M/num_ranks)
            lcr = (rank*N/num_ranks, (rank + 1)*N/num_ranks)
            m, n = (lrr[1] - lrr[0], lcr[1] - lcr[0])
            self.comm = comm
            self.num_ranks = num_ranks
            self.rank = rank
            self.M = M
            self.N = N
            self.local_row_range = lrr
            self.local_col_range = lcr
            self.m = m
            self.n = n

        # If we can't import mpi4py then continue in serial.
        except:
            pass
Esempio n. 30
0
File: IO.py Progetto: DongElkan/pyms
def save_data(file_name, data, format_str="%.6f", prepend="", sep=" ",
	compressed=False):

    """
    @summary: Saves a list of numbers or a list of lists of numbers
    to a file with specific formatting

    @param file_name: Name of a file
    @type: StringType
    @param data: A list of numbers, or a list of lists
    @type: ListType
    @param format_str: A format string for individual entries
    @type: StringType
    @param prepend: A string, printed before each row
    @type: StringType
    @param sep: A string, printed after each number
    @type: StringType
    @param compressed: A boolean. If True, the output will be gzipped
    @type: BooleanType

    @return: none
    @rtype: NoneType

    @author: Vladimir Likic
    """

    if not is_str(file_name):
        error("'file_name' is not a string")

    if not is_list(data):
        error("'data' is not a list")

    if not is_str(prepend):
        error("'prepend' is not a string")

    if not is_str(sep):
        error("'sep' is not a string")

    fp = open_for_writing(file_name)

    # decide whether data is a vector or matrix
    if is_number(data[0]):
        for item in data:
            if not is_number(item):
                error("not all elements of the list are numbers")
        data_is_matrix = 0
    else:
        for item in data:
            if not is_list(item):
                error("not all elements of the list are lists")
        data_is_matrix = 1

    if data_is_matrix:
        for ii in range(len(data)):
            fp.write(prepend)
            for jj in range(len(data[ii])):
                if is_number(data[ii][jj]):
                    fp.write(format_str % (data[ii][jj]))
                    if (jj<(len(data[ii])-1)): fp.write(sep)
                else:
                    error("datum not a number")
            fp.write("\n")
    else:
        for ii in range(len(data)):
            fp.write(prepend)
            fp.write(format_str % (data[ii]))
            fp.write("\n")

    close_for_writing(fp)

    if compressed:
        status = os.system('gzip %s' % (file_name))
        if status != 0:
            error("gzip compress failed")