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How to use parse_cmdln_args method in rester

Best Python code snippet using rester_python

continuum_removal.py

Source:continuum_removal.py

...30__license__ = 'GPLv3'31__maintainer = 'Carey Legett'32__status__ = 'Development'33__version__ = '1.0'34def parse_cmdln_args():35    """A function to parse command line arguments for this module.36    37    This function is used when this module is run as a script to parse38    commandline arguments into the appropriate variables. It also provides39    useage help information when run with the -h flag.40    41    Example:42        To invoke the help text and get information about the proper command43        line flags, run the script with the -h or --help flags.44        $ python3 continuum_removal.py -h45        or46        $ python3 continuum_removal.py --help47    48    Returns:49        args (argparse.Namespace): An object containing the state of the50        variables set via command line options. Individual elements are51        accessible with standard `args.element`_ notation.52    53    """54    parser = argparse.ArgumentParser(prog='continuum_removal.py',55                                     description=__doc__,56                                     epilog='''For more information contact 57                                     Chip at carey.legett@stonybrook.edu.''')58    parser.add_argument('-f', '--input-file', required=True,59                        help='''The name of the input file (include path if the60                        file is not in this directory).''', dest='ifile')61    parser.add_argument('-a', '--xstart', type=int, required=True,62                        help='''The x value at which to begin the continuum 63                        calculation.''', dest='xa')64    parser.add_argument('-b', '--xstop', type=int, required=True, help='''The x65                        value at which to end the continuum calculation.''',66                        dest='xb')67    group = parser.add_mutually_exclusive_group(required=True)68    group.add_argument('-d', '--delimiter', help='''The delimiter for the input69                       file. A single character representing the actual 70                       delimiter. Mutually exclusive with -w or 71                       --whitespace''', dest='delim')72    group.add_argument('-w', '--whitespace', help='''Indicates the delimiter is73                       either tabs or spaces. Mutually exclusive with -d or 74                       --delimiter.''', action='store_true', dest='whitespace')75    parser.add_argument('-n', '--skip-lines', default=0, help='''Skip this many76                        lines of the input file before reading in data.''',77                        type=int, dest='skip')78    parser.add_argument('-o', '--output-file', nargs='?', default='output.txt', 79                        help='''The name of the output file (include path 80                        if you want the file somewhere other than in the 81                        current directory). Defaults to output.txt.''',82                        dest='ofile')83    parser.add_argument('-i', '--include-input', action='store_true', dest='i',84                        help='''Write the original input data before the85                        (optional) continuum fit and continuum removed 86                        data.''')87    parser.add_argument('-c', '--continuum-output', action='store_true',88                        dest='c', help='''Write the continuum fit for each 89                        input x value after the (optional) original input data 90                        and before the continuum removed data.''')91    parser.add_argument('-v', '--verbose', action='store_true', dest='v', 92                        help='Give status information during processing.')93    94    return parser.parse_args()95def read_input_file(input_filename, input_delimiter, whitespace_flag, 96                    lines_to_skip, verbose_flag):97    """Reads the specified input file and returns a list of the data therein.98    This function reads an input file using a specified delimiter, skipping a99    given number of lines before reading. It also accepts a verbosity flag to100    enable some progress text while reading.101    Args:102        input_filename (str): The file to be read103        input_delimiter (str): The delimiter used in the input file. Set this104            to `None` if the delimiter is some form of whitespace. 105        whitespace_flag (bool): True if the delimiter is some form of106            whitespace, False otherwise. Must be false if `input_delimiter` is107            not `None`.108        lines_to_skip (int): The number of lines to skip at the beginning of109            the file before ingesting data. 110        verbose_flag (bool): True for progress output, False otherwise.111    Returns:112        data ([float,float]): A list of lists of floats containing the data113            read in from the input file.114    Raises:115        IOError: if there is a problem opening or reading the input file116        ValueError: if the data that is read from the file cannot be converted117            to a float. (e.g. the read data is not numeric)118    """119    if verbose_flag:120        print('Reading input file...')121    # Check for the version of python being used and use appropriate flags for122    # opening the input file as necessary123    if sys.version_info[0] == 2:124        raccess = 'rb'125        kwargs = {}126    else:127        raccess = 'rt'128        kwargs = {'newline': ''}129    130    try:131        with open(input_filename, raccess, **kwargs) as infile:132            if whitespace_flag:133                rawdata = [line.split() for line in itertools.islice(infile,134                           lines_to_skip, None)]135            else:136                rawdata = [line.split(input_delimiter) for line in137                           itertools.islice(infile, lines_to_skip, None)]138        if not rawdata:139            sys.exit('No data in file {}'.format(input_filename))140    except IOError as e:141        sys.exit('I/O error: file {}: {}'.format(input_filename, e))142    mydata = [[float(astring) for astring in inner] for inner in rawdata]143    # If this fails, it is likely that the data read from the input file is not144    #  numeric. It could also happen if the delimiter was not correctly145    # specified.146    return mydata147def remove_continuum(mydata, xa, xb, verbose_flag):148    """A function to remove the linear continuum between two points.149    150    This function takes a list of lists of floats containing x,y data, a151    starting x value, and an ending x value and calculates a linear fit to the152    data at those two points, extrapolated over the provided domain of x. The153    data is then normalized such that the calculated continuum equals 1. This154    can be used to prepare data for analyses such as measuring the band depth155    of absorptions in spectroscopic data.156    157    Args:158        mydata ([float, float]): A list of lists of two floats representing the159            unnormalized initial data.160        xa (float): The value of x at which to start the linear fit. This161            must be an x value in the range of the data list since the162            searching doesn't check to make sure xa falls within the bounds of163            the data.164        xb (float): The value of x at which to stop the linear fit. This165            must be an x value in the range of the data list since the166            searching doesn't check to make sure xa falls within the bounds of167            the data.168        verbose_flag (bool): True for progress output, False otherwise.169        170    Returns:171        output ([float, float]): A list of lists of two to four floats. The172            first element in each inner list will be the input x value. The 173            second element will be the input y value.  The third element will 174            be the continuum value calculated for that x. The last element 175            will be the continuum-removed y data.176    177    """178    if verbose_flag:179        print('Calculating continuum line')180    start_index = np.abs(np.array(mydata)[:, 0] - xa).argmin()181    stop_index = np.abs(np.array(mydata)[:, 0] - xb).argmin()182    startx = mydata[start_index][0]183    stopx = mydata[stop_index][0]184    starty = mydata[start_index][1]185    stopy = mydata[stop_index][1]186    187    if verbose_flag: 188        print('Start: ({!s},{!s})'.format(startx, starty))189        print('Stop: ({!s},{!s})'.format(stopx, stopy))190    191    slope = (stopy-starty)/(stopx-startx)192    intercept = starty-(slope*startx)193    194    if verbose_flag:195        print('Continuum equation: y={}*x+{}'.format(slope, intercept))196        print('Removing continuum')197    198    this_output = []199    for element in mydata:200        continuum = slope*element[0]+intercept201        crdata = element[1]/continuum202        temp_output = [element[0], element[1], continuum, crdata]203        this_output.append(temp_output)204    return this_output205def write_cont_removed_output(myoutput, output_filename, write_input_flag,206                              write_cont_flag, verbose_flag):207    """A function to write the provided list of lists of floats to a CSV file.208    209    This function writes the continuum removed data to a CSV file. Depending on210    the arguments passed, it may also write the original input data, and the211    calculated continuum for each x value.212    213    Args:214        myoutput ([float, float, float, float]): A list of lists of four floats215            that will be written, in part or in whole to the output file.216        output_filename (str): The name of the output file.217        write_input_flag (bool): True if we want to include the original data218            in the output file, False otherwise.219        write_cont_flag (bool): True if we want to include the value of the220            continuum at each x value in the output file, False otherwise.221        verbose_flag (bool): True for progress message, False otherwise.222    223    Raises:224        IOError: For any problem opening or writing to the output file.225    226    Output:227        A CSV file containing two to four columns of data as selected with the228            arguments passed to the function.229"""230    if verbose_flag:231        print('Writing output file')232    # Check for the version of python being used and use appropriate flags for233    # opening the input file as necessary234    if sys.version_info[0] == 2:235        waccess = 'wb'236        kwargs = {}237    else:238        waccess = 'w'239        kwargs = {'newline': ''}240    try:241        with open(output_filename, waccess, **kwargs) as outfile:242            writer = csv.writer(outfile)243            header = ['x']244            filtered_output = []245            for line in myoutput:246                temp = [line[0]]247                if write_input_flag:248                    temp.append(line[1])249                if write_cont_flag:250                    temp.append(line[2])251                temp.append(line[3])252                filtered_output.append(temp)253            if write_input_flag:254                header.append('original')255            if write_cont_flag:256                header.append('continuum')257            header.append(f'cont_removed{output_filename}')258            writer.writerow(header)259            writer.writerows(filtered_output)260    except IOError as e:261        sys.exit('Output file error: {}, {}'.format(e, sys.exc_info()))262if __name__ == '__main__':263    args = parse_cmdln_args()264    data = read_input_file(args.ifile, args.delim, args.whitespace, args.skip,265                           args.v)266    output = remove_continuum(data, float(args.xa), float(args.xb), args.v)...

wl_to_wn.py

Source:wl_to_wn.py

...29__maintainer = 'Carey Legett'30__status__ = 'Development'31__version__ = '0.1a'32ureg = UnitRegistry()33def parse_cmdln_args():34    """A function to parse command line arguments for this module.35    This function is used when this module is run as a script to parse36    commandline arguments into the appropriate variables. It also provides37    useage help information when run with the -h flag.38    Example:39        To invoke the help text and get information about the proper command40        line flags, run the script with the -h or --help flags.41        $ python3 continuum_removal.py -h42        or43        $ python3 continuum_removal.py --help44    Returns:45        args (argparse.Namespace): An object containing the state of the46        variables set via command line options. Individual elements are47        accessible with standard `args.element`_ notation.48    """49    parser = argparse.ArgumentParser(prog='wl_to_wn.py',50                                     description=__doc__,51                                     epilog='''For more information contact 52                                     Chip at carey.legett@stonybrook.edu.''')53    parser.add_argument('-f', '--input-file', required=True,54                        help='''The name of the input file (include path if the55                        file is not in this directory).''', dest='ifile')56    parser.add_argument('-x', '--xunits', type=str, required=True,57                        help='''The units that the x data are in (e.g. 58                        'micrometers' or 'wavenumbers'.''', dest='xunits')59    group = parser.add_mutually_exclusive_group(required=True)60    group.add_argument('-d', '--delimiter', help='''The delimiter for the input61                       file. A single character representing the actual 62                       delimiter. Mutually exclusive with -w or 63                       --whitespace''', dest='in_delim')64    group.add_argument('-w', '--whitespace', help='''Indicates the delimiter is65                       either tabs or spaces. Mutually exclusive with -d or 66                       --delimiter.''', action='store_true', dest='whitespace')67    parser.add_argument('-n', '--skip-lines', default=0, help='''Skip this many68                            lines of the input file before reading in data.''',69                        type=int, dest='skip')70    parser.add_argument('-o', '--output-file', nargs='?', default='output.txt',71                        help='''The name of the output file (include path 72                        if you want the file somewhere other than in the 73                        current directory). Defaults to output.txt.''',74                        dest='ofile')75    parser.add_argument('-s', '--output-delimiter', required=False, help='''The76                        delimiter to be used in the output file. Defults to tab77                        .''', dest='out_delim')78    parser.add_argument('-v', '--verbose', action='store_true', dest='v',79                        help='Give status information during processing.')80    return parser.parse_args()81def read_input_file(filename, delimiter, whitespace_flag, skip_lines, xunits,82                    verbose):83    if verbose:84        print('Reading input file...')85    try:86        with open(filename, 'rt', newline='') as infile:87            if whitespace_flag:88                rawdata = [line.split() for line in89                           itertools.islice(infile, skip_lines, None)]90            else:91                rawdata = [line.split(delimiter) for line in92                           itertools.islice(infile, skip_lines, None)]93        if not rawdata:94            sys.exit('No data in file {}'.format(filename))95    except IOError as e:96        sys.exit('I/O error: file {}: {}'.format(filename, e))97    mydata = [[float(astring) for astring in inner] for inner in rawdata]98    if verbose:99        print('Assigning units.')100    mydata = [[row[0] * ureg[f'{xunits}'], row[1]] for row in mydata]101    # If this fails, it is likely that the data read from the input file is not102    #  numeric. It could also happen if the delimiter was not correctly103    # specified.104    if verbose:105        print('Done with input.')106    return mydata107def write_to_output(somedata, out_filename, out_delim, verbose_flag):108    if verbose_flag:109        print('Writing output file')110    try:111        with open(out_filename, 'w', newline='') as outfile:112            writer = csv.writer(outfile, delimiter=out_delim)113            header = ['wn', 'data']114            writer.writerow(header)115            writer.writerows(somedata)116    except IOError as e:117        sys.exit(f'Output file error: {e}, {sys.exc_info()}')118if __name__ == '__main__':119    args = parse_cmdln_args()120    x = ureg[f'{args.xunits}']121    data = read_input_file(args.ifile, args.in_delim, args.whitespace,122                           args.skip, args.xunits, args.v)123    data = [[line[0].to(1 / ureg.centimeter, 'sp').magnitude, line[1]] for line in data]...

apirunner.py

Source:apirunner.py

2import argparse3import logging4import sys5DEFAULT_TEST_CASE = 'test_case.json'6def parse_cmdln_args():7    parser = argparse.ArgumentParser(description='Process command line args')8    parser.add_argument('--log', help='log help', default='INFO')9    parser.add_argument(10        '--tc', help='tc help')11    parser.add_argument(12        '--ts', help='ts help')13    args = parser.parse_args()14    return (args.log.upper(), args.tc, args.ts)15def run():16    log_level, test_case_file, test_suite_file = parse_cmdln_args()17    print log_level, test_case_file, test_suite_file18    logging.basicConfig()19    logger = logging.getLogger('rester')20    logger.setLevel(log_level)21    test_runner = ApiTestCaseRunner()22    if test_case_file is not None:23        print "test case has been specified"24        test_runner.run_test_case(test_case_file)25    elif test_suite_file is not None:26        print "test suite has been specified"27        test_runner.run_test_suite(test_suite_file)28    else:29        print "running the default test case"30        test_runner.run_test_case(DEFAULT_TEST_CASE)...

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