Commit d6b65567 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

python 3.7/3.9 fixes

parent e4dc1fd5

pysen/echo/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -4,4 +4,4 @@ echo fit/plot module 


from .fit    import fit_echo_current, Spectrum       # NOQA

from .reduce import get_symmetry_phase, reduce_echo  # NOQA

from .make_phase_table import make_phase_table       # NOQA
 
from .phase_table import make_phase_table            # NOQA

pysen/plot/nseplot.py

+39 −29
Original line number Diff line number Diff line
@@ -4,12 +4,12 @@ nseplot: command line interface to pysen modules 


"""

import sys

import time

import os.path

import argparse

import functools

import logging

import h5py

import time



import numpy as np

import matplotlib as mpl
@@ -146,27 +146,30 @@ def action_qtau(filenames, **kwargs): 
        plt.savefig(savefig)



def action_phase_table(filenames, **kwargs):

    """"""

    "action for phase table plots"

    phtab = None

    log = logging.getLogger()

    outdir    = kwargs.pop('outdir')

    savefig   = kwargs.pop('savefig')

    savefile  = kwargs.pop('savefile')

    polyfit   = kwargs.pop('polyfit')

    pos       = kwargs.pop('pos')

    threshold = kwargs.pop('threshold')

    for filename in filenames:

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

        if ext==".echo":

            hfile = convert_to_hdf(filename, '.', data_type='echo')

        else:

            hfile = filename

        log.info('======> input data %s', filename)

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

        try:

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

            if ext != ".h5":

                filename = convert_to_hdf(filename, outdir, data_type='echo')

            log.info('======> input data %s', basename)

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

                res = get_symmetry_phase(hdf5file, **kwargs)

                if phtab is None:

                    phtab = res

                else:

                    phtab = np.vstack((phtab,res))

        except (OSError, RuntimeError) as exc:

            log.error("%s",exc)

            return



    plt.figure(figsize=(12,5))

    i00, phi, phase, max_diff = make_phase_table(phtab, polyfit, pos=pos, threshold=threshold)
@@ -197,7 +200,7 @@ def action_phase_table(filenames, **kwargs): 
            sys.stdout = orig_stdout



    if savefile:

        with open(savefile, 'w+') as fd:

        with open(savefile, 'w+', encoding='ascii') as fd:

            print_phase_table(fd)

    else:

        print_phase_table()
@@ -219,7 +222,7 @@ def arguments_common(): 
    pars.add_argument('--save-figure', '-S', dest='savefig', metavar='file',

                        help='save figure to a file (do not show)')

    pars.add_argument('--save-file', '-s', dest='savefile', metavar='file',

                        help='save data to a file')

                        help='save output data to a file')

    # mutually exclusive [ -v | -q ]

    verbose = pars.add_mutually_exclusive_group()

    verbose.add_argument('--verbose', '-v', dest='loglevel', action='count',
@@ -425,10 +428,17 @@ def add_qtau_options(subparser, parents=None): 
                        help='set instrument position: (default %(default)s)')

    pars.add_argument('--mode', '-m', dest='mode', choices=INST_MODES,

                        help='set instrument (default %(default)s)')

    try: # extend is only available in python 3.8 and newer

        pars.add_argument('--taus',  metavar='tau',  type=float, nargs='*', action='extend',

                        help='select list of taus')

        pars.add_argument('--tbins', metavar='tbin', type=int,   nargs='*', action='extend',

                        help='select list of tbins')

    except ValueError:

        pars.add_argument('--taus',  metavar='tau',  type=float, nargs='*', action='append',

                        help='select list of taus')

        pars.add_argument('--tbins', metavar='tbin', type=int,   nargs='*', action='append',

                        help='select list of tbins')





    grp = pars.add_argument_group('presentation options')

    grp.add_argument('--title',  dest='title', help='set plot title')
@@ -448,18 +458,18 @@ def add_qtau_options(subparser, parents=None): 
def add_ptab_options(subparser, parents=None):

    "make phase table"

    pars = subparser.add_parser('phase_table', parents=parents,

                       help='phase table',

                       description='phase table')

                     help='phase table', description='phase table')

    pars.set_defaults(pos='p2', polyfit=2, threshold=0.2)

    # defaults

    pars.set_defaults(tbin1=4, tbin2=38, xpix1=5, xpix2=27, ypix1=5, ypix2=27)

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

    pars.add_argument('--pos' , '-p', dest='pos',  choices=INST_POSITIONS,

                     help='set instrument position: (default %(default)s)')

    pars.add_argument('--polyfit', '-f', dest='polyfit', type=int,

                     help='use polyfit')

    pars.add_argument('--threshold', dest='threshold', metavar='thr', type=float,

                     help='clustering threshold (advanced option)')

    pars.add_argument('--poly', '-P', dest='polyfit', metavar='deg', type=int,

                     help='use polynomial fit of degree (default %(default)s)')

    pars.add_argument('--threshold', dest='threshold', metavar='thres', type=float,

                     help=argparse.SUPPRESS)

                     #help='clustering threshold (advanced option)')



# ============================================================================================

# the main command line interface

pysen/revision.py

+1 −1
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ PySEN revision module 
"""

import sys

__version__  = "0.76"

__release__  = "dev1"

__release__  = "dev2"

__date__     = "Aug 19, 2022"



def version(full=False):