Exemple #1
0
    def __set_time(self, time_list):

        """
        @summary: Sets time-related properties of the data

        @param time_list: List of retention times
        @type time_list: ListType

        @author: Vladimir Likic
        """

        # calculate the time step, its spreak, and along the way
        # check that retention times are increasing
        time_diff_list = []

        for ii in range(len(time_list)-1):
            t1 = time_list[ii]
            t2 = time_list[ii+1]
            if not t2 > t1:
                error("problem with retention times detected")
            time_diff = t2 - t1
            time_diff_list.append(time_diff)

        time_step = mean(time_diff_list)
        time_step_std = std(time_diff_list)

        self.__time_list = time_list
        self.__time_step = time_step
        self.__time_step_std = time_step_std
        self.__min_rt = min(time_list)
        self.__max_rt = max(time_list)
Exemple #2
0
    def __set_time(self, time_list):

        """
        @summary: Sets time-related properties of the data

        @param time_list: List of retention times
        @type time_list: ListType

        @author: Vladimir Likic
        """

        # calculate the time step, its spreak, and along the way
        # check that retention times are increasing
        time_diff_list = []

        for ii in range(len(time_list)-1):
            t1 = time_list[ii]
            t2 = time_list[ii+1]
            if not t2 > t1:
                error("problem with retention times detected")
            time_diff = t2 - t1
            time_diff_list.append(time_diff)

        time_step = mean(time_diff_list)
        time_step_std = std(time_diff_list)

        self.__time_list = time_list
        self.__time_step = time_step
        self.__time_step_std = time_step_std
        self.__min_rt = min(time_list)
        self.__max_rt = max(time_list)
Exemple #3
0
    def info(self, print_scan_n=False):

        """
        @summary: Prints some information about the data

        @param print_scan_n: If set to True will print the number
            of m/z values in each scan
        @type print_scan_n: BooleanType

        @author: Vladimir Likic
        """

        # print the summary of simply attributes
        print " Data retention time range: %.3f min -- %.3f min" % \
                (self.__min_rt/60.0, self.__max_rt/60)
        print " Time step: %.3f s (std=%.3f s)" % ( self.__time_step, \
                self.__time_step_std )
        print " Number of scans: %d" % ( len(self.__scan_list) )
        print " Minimum m/z measured: %.3f" % ( self.__min_mass )
        print " Maximum m/z measured: %.3f" % ( self.__max_mass )

        # calculate median number of m/z values measured per scan
        n_list = []
        for ii in range(len(self.__scan_list)):
            scan = self.__scan_list[ii]
            n = len(scan)
            n_list.append(n)
            if print_scan_n: print n
        mz_mean = mean(n_list)
        mz_median = median(n_list)
        print " Mean number of m/z values per scan: %d" % ( mz_mean )
        print " Median number of m/z values per scan: %d" % ( mz_median )
Exemple #4
0
    def info(self, print_scan_n=False):

        """
        @summary: Prints some information about the data

        @param print_scan_n: If set to True will print the number
            of m/z values in each scan
        @type print_scan_n: BooleanType

        @author: Vladimir Likic
        """

        # print the summary of simply attributes
        print " Data retention time range: %.3f min -- %.3f min" % \
                (self.__min_rt/60.0, self.__max_rt/60)
        print " Time step: %.3f s (std=%.3f s)" % ( self.__time_step, \
                self.__time_step_std )
        print " Number of scans: %d" % ( len(self.__scan_list) )
        print " Minimum m/z measured: %.3f" % ( self.__min_mass )
        print " Maximum m/z measured: %.3f" % ( self.__max_mass )

        # calculate median number of m/z values measured per scan
        n_list = []
        for ii in range(len(self.__scan_list)):
            scan = self.__scan_list[ii]
            n = len(scan)
            n_list.append(n)
            if print_scan_n: print n
        mz_mean = mean(n_list)
        mz_median = median(n_list)
        print " Mean number of m/z values per scan: %d" % ( mz_mean )
        print " Median number of m/z values per scan: %d" % ( mz_median )