added autoconversion to HDF

#!/usr/bin/env python

"ATARI Plot"

from   os.path import basename, splitext

import os.path 

import logging

import numpy as np

import h5py

import matplotlib.pyplot as plt

from pysen import ANGSTROM, NANOSECOND

from pysen import ANGSTROM, NANOSECOND, version

from pysen.io import read_echo, HdfConverter

from pysen.atarilib import fit_echo_current, Spectrum

def echo_convert(filename):

    schema=None

    compression='gzip'

    mode='w'

    outdir='.'

    log = logging.getLogger()

    outfile, _ = os.path.splitext(os.path.basename(filename))

    outfile = os.path.join(outdir, outfile + ".h5")

    converter = HdfConverter(outfile, mode=mode, version=version())

    log.debug('converting echo %s => %s', filename, outfile)

    data = read_echo(filename)

    converter.write(data, compression=compression, schema=schema)

    log.info('written HDF5 file %s', outfile)

    return outfile

def echo_plot(hdfile, iecho=0, **kwargs):

    "echo plot"

    ypix1   = kwargs.pop('ypix1', 10)

    ypix2   = kwargs.pop('ypix2', 22)

    base    = splitext(basename(hdfile.filename))[0]

    base    = os.path.splitext(os.path.basename(hdfile.filename))[0]

    comment = hdfile.attrs['master_comment']

    comment = comment.decode("utf-8")

                #    plt.text(0.01, 1.01, r'$R(Q,t)$=%.3g' % R, transform=ax.transAxes)

                #ax.axhline(np.average(up))

                #ax.axhline(np.average(dn))

        #plt.xlabel(r'phase current [A]')

        #plt.xlabel(r'ephase current [A]')

        #plt.legend(loc='best')

        #plt.grid(True)

    "the main"

    import argparse

    parser = argparse.ArgumentParser(description='atari plot')

    parser = argparse.ArgumentParser(description='echo plot')

    parser.set_defaults(loglevel=logging.INFO)

    parser.add_argument('file', metavar='filename', help='file to process', nargs='+')

    parser.add_argument('--echo',  '-e',  dest='echo', type=int,   default=None,

                        help='set echo to display (default=%(default)s)')

                        help='set min TOF bin (default=%(default)s)')

    parser.add_argument('--t2',  '-T',  dest='tbin2', type=int,   default=None,

                        help='set max TOF bin (default=%(default)s)')

    parser.add_argument('--verbose', '-v', dest='loglevel', action='store_const',

                        const=logging.DEBUG,  help='verbose output')

    parser.add_argument('--quiet', '-q', dest='loglevel', action='store_const',

                        const=logging.WARNING,  help='verbose output')

    parser.add_argument('--version', action='version',

                        version='%(prog)s pysen={version}'.format(version=version(full=True)))

    parser.add_argument('--only-echo', '-N', dest='only_echo', action='store_true',   default=False,

                        help='show only echo (no up/down)')

    args = parser.parse_args()

    if args.loglevel>=logging.INFO:

        log_format=r'%(message)s'

    else:

        log_format=r'%(levelname)s: %(funcName)s: %(message)s'

    logging.basicConfig(level=args.loglevel, format=log_format)

    log = logging.getLogger()

    kwargs = vars(args)

    for filename in args.file:

        basename , ext = os.path.splitext(os.path.basename(filename))

        if ext==".echo":

            log.info('converting %s to HDF', basename)

            outfile = echo_convert(filename)

            filename = outfile

        with h5py.File(filename, 'r') as hdf5file:

            echo_plot(hdf5file, iecho=args.echo, **kwargs)

    plt.show()