Commit cc4e3767 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

bugfixes 

- echo/atari: crash when dealing with 'non-echo' scans
- atari: formatting issue when displaying atari plots
parent 626a3106

pysen/inout/hdf.py

+6 −4
Original line number Diff line number Diff line
@@ -215,12 +215,12 @@ def convert_to_hdf(filename, outdir, **kwargs): 
    log = logging.getLogger()

    #

    basename = os.path.basename(filename)

    filetype = get_nsefiletype(filename)

    if filetype=='application/nse-echo-hdf':

    file_type = get_nsefiletype(filename)

    if file_type=='application/nse-echo-hdf':

        log.info('file %s already converted to HDF5', basename)

        return filename

    #

    outfile  = make_h5filename(basename, outdir=outdir, filetype=filetype)

    outfile  = make_h5filename(basename, outdir=outdir, filetype=file_type)

    log.info('converting %s to HDF5', basename)

    if not overwrite and is_file_newer(outfile, filename):

        log.info('file %s is newer than %s', outfile, filename)
@@ -229,9 +229,11 @@ def convert_to_hdf(filename, outdir, **kwargs): 
    # convert to h5

    converter = HdfConverter(version=version_info())

    if data_type is None: # guess data type based on file

        reader = DATA_READER.get(filetype)

        reader = DATA_READER.get(file_type)

    else: # data type given

        reader = DATA_READER.get(data_type)

    if reader is None:

        raise RuntimeError(f"Don't know how to handle {file_type} file")

    converter.data = reader(filename)

    converter.write(outfile, mode=mode, compression=compression)

    return outfile

pysen/plot/nseplotlib.py

+14 −2
Original line number Diff line number Diff line
@@ -281,7 +281,7 @@ def plot_atari(hdfile, iecho=None, **kwargs): 
        p = ax.errorbar(cur[:nph], pha, yerr=epha, fmt='.', lw=1)

        dcol = p[0].get_color()

        ax.plot(xef, yef, '--')

        ax.axvline(phase0,   color='blue',  lw=1, ls='--', label=rf'{phase0:.4fA}' )

        ax.axvline(phase0,   color='blue',  lw=1, ls='--', label=rf'{phase0:.4f}' )

        ax.axvline(phase_ef, color='red',   lw=2, ls='-',

                   label=rf'({phase_ef:.4f}$\pm${phase_err:.2g})')
@@ -671,8 +671,20 @@ def action_default(filenames, **kwargs): 
    taus    = kwargs.pop('taus')

    savefig = kwargs.pop('savefig')

    log = logging.getLogger()

    new_filenames = []



    # FIX THIS MESSS

    for filename in filenames:

        try:

            outfile = convert_files(filename, converter='from_taco', **kwargs)

            new_filenames.extend(outfile)

        except (OSError,RuntimeError) as exc:

            log.error("%s",format(exc))

        except KeyboardInterrupt:

            break



    try:

        for filename in convert_files(*filenames, converter='from_taco', **kwargs):

        for filename in new_filenames:

            basename = os.path.basename(filename)

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

                action(hdf5file, taus, **kwargs)