How to use the pythoms.scripttime.ScriptTime function in pythoms

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github larsyunker / PythoMS / PyRSIR.py View on Github external
if 'formula' in dct[species] and dct[species]['formula'] is not None:
                try:
                    dct[species]['mol'].res = res  # sets resolution in Molecule object
                except NameError:
                    res = int(mzml.auto_resolution())
                    dct[species]['mol'].res = res
                # dct[species]['mol'].sigma = dct[species]['mol'].sigmafwhm()[1]  # recalculates sigma with new resolution
                dct[species]['bounds'] = dct[species]['mol'].bounds  # caclulates bounds
        return dct

    # ----------------------------------------------------------
    # -------------------PROGRAM BEGINS-------------------------
    # ----------------------------------------------------------

    if verbose is True:
        stime = ScriptTime()
        stime.printstart()

    n = check_integer(n, 'number of scans to sum')  # checks integer input and converts to list

    if type(xlsx) != dict:
        if verbose is True:
            sys.stdout.write('Loading processing parameters from excel file')
            sys.stdout.flush()
        xlfile = XLSX(xlsx, verbose=verbose)
        sp = xlfile.pullrsimparams()
    else:  # if parameters were provided in place of an excel file
        sp = xlsx

    mskeys = ['+', '-']
    for key in sp:
        if 'formula' in sp[key] and sp[key]['formula'] is not None:  # if formula is specified
github larsyunker / PythoMS / pythoms / molecule.py View on Github external
abbrv_spec.loader.exec_module(abbrv_module)
    user_abbrvs = abbrv_module.user_abbrvs
    abbrvs.update(user_abbrvs)
except FileNotFoundError:  # if it can't find the file, continue with default abbreviations
    pass


"""Mass dictionary associated with the instance"""
MASS_KEY = 'crc_mass'
mass_dict = getattr(
    mass_dictionaries,
    MASS_KEY,
)


st = ScriptTime(profile=True)

# valid start and end brackets
OPENING_BRACKETS = ['(', '{', '[']  # opening brackets
CLOSING_BRACKETS = [')', '}', ']']  # closing brackets
SIGNS = ['+', '-']  # charge signs
VERBOSE = False  # toggle for verbose

# valid grouping methods
VALID_GROUP_METHODS = [
    'weighted',
    'centroid',
]
# valid isotope pattern generation methods
VALID_IPMETHODS = [
    'combinatorics',
    'multiplicative',
github larsyunker / PythoMS / spectrum binner.py View on Github external
def bin_spectra(filename, start=None, end=None, save=True, dec=3):
    """
    Sums spectra from raw file and outputs to excel file

    :param filename: raw or mzML filename
    :param start: start scan (None will default to 1)
    :param end: end scan (None will default to the last scan)
    :param save: whether to save into an excel document (if a string is provided, that filename will be used)
    :param dec: decimal places to track when binning the spectrum
    :return: paired x, summed y lists
    """

    st = ScriptTime()
    st.printstart()
    mzml = mzML(filename)  # create mzML object
    if start is None:
        start = mzml.functions[1]['sr'][0] + 1
    if end is None:
        end = mzml.functions[1]['sr'][1] + 1
    x, y = mzml.sum_scans(
        start=start,
        end=end,
        dec=dec,
    )
    if save is not False:
        if type(save) == str:  # if a filename was provided for the Excel file
            xlfile = XLSX(save, create=True)
        else:  # otherwise use the mzML filename
            xlfile = XLSX(filename, create=True)
github larsyunker / PythoMS / pythoms / scripttime.py View on Github external
self.profiles[fn.__name__][1].append(elapsed_time)
            return ret  # returns the calculated call of the function

        if self.profile is True:
            return with_profiling  # returns the decorated function
        else:
            return fn

    def triggerend(self):
        """triggers endpoint and calculates elapsed time since start"""
        self._end_seconds = time.time()
        self._end_clock = time.localtime()


if __name__ == '__main__':
    st = ScriptTime()
    time.sleep(2.)
    st.triggerend()
    st.printend()