Commit 7b6fdcba authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

added nseplot dtrfile, fixes in transmission plot

parent a7579e82

pysen/inout/reader.py

+12 −5
Original line number Diff line number Diff line
@@ -776,20 +776,27 @@ def read_transmission(filename): 
    #transtab = { '"' : None,

    #             '\n': None, }

    with open(filename, mode='r', encoding='ascii') as _fdesc:

        lines = _fdesc.readlines()

        header = remove_chars(lines[1], delchars='"\n')



        lines = iter(_fdesc.readlines())

        prevline = None

        while True:

            line = next(lines)

            if line.startswith('"detector.sum'):

                break;

            prevline = line

        header = remove_chars(prevline, delchars='"\n')

        result['header']     = header

        header = header.split(',')

        result['proposal'  ] = header[0]

        result['sample'    ] = header[1].split()[-1]

        result['wavelength'] = _evaluate(header[2].split()[-1])

        thead = remove_chars(lines[2], delchars='"\n').split()

        tdata = remove_chars(lines[3], delchars='"\n').split()

        thead = remove_chars(line, delchars='"\n').split()

        tdata = remove_chars(next(lines), delchars='"\n').split()

        for k,v in zip(thead, tdata):

            result[k] = _evaluate(v)

        tmpkey = None

        tmparr = []

        for line in lines[4:]:

        for line in lines:

            line = remove_chars(line, delchars='"\n').strip()

            if not line:

                continue

pysen/plot/__init__.py

+2 −1
Original line number Diff line number Diff line
@@ -3,7 +3,8 @@ plotting subpackage 
"""

from .plotutil    import get_nsubplots                               # NOQA

from .qplot       import ( plot_coverage, plot_curscan,              # NOQA

                           plot_diffrun , plot_transmission)         # NOQA

                           plot_diffrun , plot_transmission,         # NOQA

                           plot_datreat)                             # NOQA

from .echo        import plot_single_echo, echo_plot, atari_plot     # NOQA

from .histplotlib import plot_var, plot_sc                           # NOQA

from .nseplotlib  import ( plot_atari, plot_echo,                    # NOQA

pysen/plot/nseplot.py

+57 −39
Original line number Diff line number Diff line
@@ -12,9 +12,8 @@ from pysen import version, setup_logger 
from pysen.config import DEFAULT_ACCELERATOR_POWER

from pysen.inout  import convert_to_hdf

from pysen.plot   import ( plot_echo, plot_atari, plot_map, 

                           plot_xyz,

                           plot_magnetic_fields,

                           plot_diffrun, plot_transmission )

                           plot_xyz, plot_magnetic_fields,

                           plot_diffrun, plot_transmission, plot_datreat)

#from pysen.plot.cmdline import NsePlotApp



def action_default(filenames, **kwargs):
@@ -77,7 +76,7 @@ def action_diffrun(filenames, **kwargs): 
def action_transmission(filenames, **kwargs):

    "action for transmission"

    savefig       = kwargs.pop('savefig')

    spectrum_only = kwargs.pop('spectrum_only')

    spectrum_only = kwargs.get('spectrum_only')

    #log = kwargs.pop('log')

    to_show = True

    ax1 = None
@@ -96,8 +95,17 @@ def action_transmission(filenames, **kwargs): 
        to_show = True

    return to_show





#def action_qtau(, **kwargs):

def action_datreat(filenames, **kwargs):

    "action for datreat"

    savefig = kwargs.pop('savefig')

    #log = kwargs.pop('log')

    _, axis = plt.subplots(figsize=(8,8))

    plot_datreat(axis, filenames, **kwargs)

    if savefig:

        plt.savefig(savefig)

    else:

        to_show = True

    return to_show
@@ -131,6 +139,12 @@ def arguments_vertscale(pars): 
    pars.add_argument('--normalize', '-n' , dest='normalize', action='store_true',

                           help='normalize results')



def add_subparser(name, parent, sub, helpmsg=None, filearg=None):

    parser_name = sub.add_parser(name, help=helpmsg, parents=[parent])

    if filearg:

        parser_name.add_argument('file', metavar='filename', help='file to process', nargs=filearg)

    return parser_name.add_argument_group()



def main():

    "the main"
@@ -140,7 +154,7 @@ def main(): 
    parser_top.set_defaults(loglevel=1, outdir='.')

    parser_top.add_argument('--version', '-V', action='version',

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

    subparsers  = parser_top.add_subparsers(dest='what', required=True, help='what to plot')

    subparsers  = parser_top.add_subparsers(dest='plot', required=True, help='what to plot')



    # common arguments

    parser = argparse.ArgumentParser(add_help=False)
@@ -152,27 +166,23 @@ def main(): 
                        center_only=False, whole_detector=False,

                        map_type='all', phase0=None,

                        incoherent=False, max_chi2=1e3)

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

    parser.add_argument('--save-figure', '-S', dest='savefig',

    # version option

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

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

    #

    parser.add_argument('--save-figure', '-S', dest='savefig', metavar='file',

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

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

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

                        help='save data to a csv file')

    # mutually exclusive [ -v | -q ]

    group_vrb = parser.add_mutually_exclusive_group()

    group_vrb.add_argument('--verbose', '-v', dest='loglevel', action='count',

                           help='verbose output')

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

                           const=0,  help='verbose output')

    # version option

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

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



                           const=0,  help='suppres output')



    # echo plot

    parser_echo = subparsers.add_parser('echo', help='plot echo (.echo or .h5 files)', parents=[parser])

    grp_echo = parser_echo.add_argument_group('echo plot options')

    grp_echo.add_argument('--tau', '-t',  dest='tau', type=int,

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

    grp_echo=add_subparser('echo', parser, subparsers, helpmsg='plot echo (.echo or .h5 files)', filearg='+')

    grp_echo.add_argument('--center-only'   , '-C', dest='center_only', action='store_true',

                          help='show only center patch')

    grp_echo.add_argument('--only-echo', dest='only_echo', action='store_true',
@@ -187,8 +197,7 @@ def main(): 
    grp_echo.add_argument('--resolution', '-R', dest='resolution_plot', action='store_true',

                          help='TBD')

    # atari plot

    parser_atari  = subparsers.add_parser('atari',  help='atari plot (.echo or .h5 files)', parents=[parser])

    grp_atari = parser_atari.add_argument_group('atari plot options')

    grp_atari=add_subparser('atari', parser, subparsers, helpmsg='atari plot (.echo or .h5 files)', filearg='+')

    grp_atari.add_argument('--tau', '-t',  dest='tau', type=int,

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

    arguments_selection(grp_atari)
@@ -201,9 +210,7 @@ def main(): 
                           help='set inital phase for echo fitting (default=%(default)s)')



    # xyz plot

    parser_xyz = subparsers.add_parser('xyz', help='plot xyz analysis (.dat or .h5 files)', parents=[parser])

    grp_xyz= parser_xyz.add_argument_group('xyz analysis plot options')



    grp_xyz=add_subparser('xyz', parser, subparsers, helpmsg='plot xyz analysis (.dat or .h5 files)', filearg='+')

    grp_xyz.set_defaults(overwrite=False, qmin=0, qmax=np.inf, deltaq=0.001)

    arguments_selection(grp_xyz)

    arguments_vertscale(grp_xyz)
@@ -214,8 +221,7 @@ def main(): 
    grp_xyz.add_argument('--delta-q', dest='deltaq', type=float,

                           help='q histogram bin witdth')

    # diffraction plot

    parser_diffrun = subparsers.add_parser('diffrun', help='plot diffraction scan', parents=[parser])

    grp_diffrun= parser_diffrun.add_argument_group('diffraction scan plot options')

    grp_diffrun=add_subparser('diffrun', parser, subparsers, helpmsg='plot diffraction scan(s)', filearg='+')

    grp_diffrun.set_defaults(selection=None, power=DEFAULT_ACCELERATOR_POWER)

    grp_diffrun.add_argument('--up',      '-u', dest='selection', action='append_const', const='up',

                       help="plot 'up' counts")
@@ -239,8 +245,7 @@ def main(): 
                        help="use attenuation table")



    # transmission plot

    parser_trans = subparsers.add_parser('transmission', help='plot transmission data', parents=[parser])

    grp_trans= parser_trans.add_argument_group('transmission plot options')

    grp_trans=add_subparser('transmission', parser, subparsers, helpmsg='plot transmission data', filearg='+')

    grp_trans.set_defaults(log_scale=False, spectrum_only=False, pos='p2')

    grp_trans.add_argument('--pos' , '-p', dest='pos' ,

                           help='set instrument position: p1, p2, p3 or p4 (default %(default)s)')
@@ -254,9 +259,16 @@ def main(): 
    grp_trans.add_argument('--echodet', '-e', dest='echodet', action='store_true',

                        help='report transmission for echodet 1/T')



    # datreat plot

    grp_dtr=add_subparser('datreat', parser, subparsers, helpmsg='plot datreat files (.dtr or .dat)', filearg='+')

    grp_dtr.add_argument('--logt', dest='logt', action='store_true',

                        help='set log scale for tau')

    grp_dtr.add_argument('--logs', dest='logs', action='store_true',

                        help='set log scale for S(Q,tau)')

    grp_dtr.add_argument('--prune', dest='prune', action='store_true',

                        help='prune data')

    # map plot

    parser_map = subparsers.add_parser('maps', help='plot maps (.echo or .h5 files)', parents=[parser])

    grp_map = parser_map.add_argument_group('map plot options')

    grp_map=add_subparser('maps', parser, subparsers, helpmsg='plot echo maps (.echo or .h5)', filearg='+')

    grp_map.add_argument('--tau', '-t',  dest='tau', type=int,

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

    grp_map.add_argument('--map-type', dest='map_type', choices=['all', 'up', 'down'],
@@ -264,8 +276,7 @@ def main(): 
    grp_map.add_argument('--num-pix', '-N', dest='npix', type=int,

                         help='set pixel binning (default=%(default)s)')

    # magnetic field

    parser_bfield = subparsers.add_parser('bfield', help='plot magnetic fields (.echo or .h5 files)', parents=[parser])

    grp_bfield = parser_bfield.add_argument_group('magnetic field plot options')

    grp_bfield=add_subparser('bfield', parser, subparsers, helpmsg='plot magnetic fields (.echo or .h5)', filearg='+')

    grp_bfield.add_argument('--tau', '-t',  dest='tau', type=int,

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

    grp_bfield.add_argument('--max-chi2', dest='max_chi2', type=float, default=1e-2,
@@ -273,31 +284,38 @@ def main(): 
    grp_bfield.add_argument('--axis', dest='axis', type=int, default=-1,

                            help='set axis to plot  (default=%(default)s)')



    # qtau plot

    #grp_qtau=add_subparser('qtau', parser, subparsers, helpmsg='plot q-tau coverage', filearg='?')



    # phase table

    #grp_ptab=add_subparser('phase_table', parser, subparsers, helpmsg='make phase table from echo files (.echo or .h5)', filearg='+')



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

    args = parser_top.parse_args()

    log = setup_logger(args.loglevel)

    log.debug('program arguments %s', args)



    #if not args.what:

    #if not args.plot

    #    NsePlotApp().cmdloop()

    #    return





    plt.rcParams.update({'figure.max_open_warning': 0})

    if args.savefig:

        plt.switch_backend('Agg')



    kwargs = vars(args)



    if args.what in ('echo', 'atari', 'maps', 'bfield'):

        plot_action = dict(echo=plot_echo, atari=plot_atari, maps=plot_map, bfield=plot_magnetic_fields).get(args.what)

    if args.plot in ('echo', 'atari', 'maps', 'bfield'):

        plot_action = dict(echo=plot_echo, atari=plot_atari, maps=plot_map, bfield=plot_magnetic_fields).get(args.plot)

        to_show = action_default(args.file, action=plot_action, log=log, **kwargs)

    if args.what in ('xyz', ):

    if args.plot in ('xyz', ):

        to_show = action_xyz(args.file, log=log, **kwargs)

    if args.what in ('diffrun', ):

    if args.plot in ('diffrun', ):

        to_show = action_diffrun(args.file, log=log, **kwargs)

    if args.what in ('transmission', ):

    if args.plot in ('transmission', ):

        to_show = action_transmission(args.file, log=log, **kwargs)

    if args.plot in ('datreat', ):

        to_show = action_datreat(args.file, log=log, **kwargs)

    if to_show:

        plt.show()

pysen/plot/qplot.py

+65 −1
Original line number Diff line number Diff line
@@ -7,6 +7,7 @@ import time 
import os

import logging

import collections

import itertools

import numpy as np



from matplotlib import cm
@@ -18,7 +19,7 @@ from scipy.spatial import ConvexHull 


from .. import ANGSTROM

from ..config import PCHARGE_PER_SECOND, wavelength_bandwitdh

from ..inout  import read_datfile, read_diffrun, read_transmission

from ..inout  import read_datfile, read_diffrun, read_transmission, read_datreat





COLOR_MAP = { 0: None,
@@ -482,3 +483,66 @@ def plot_transmission(ax0, ax1, filenames, **kwargs): 
        ax1.set_ylabel('T0/Tsam')

    ax1.grid(True)

    return





def _prune_data(data, min_points=3, min_taus=3, max_err=1.0):

    """

    Prune/cleanup DrSPINE reduced data



    """

    if len(data)<=0:

        return None

    data =  data.T

    data = data[data[:,5]>min_points] # at least min_points contributing points

    data = data[data[:,4]>0] # var(tau)

    data = data[data[:,3]>0] # var(sqt)

    data = data[data[:,2]>0] # err(sqt)

    data = data[data[:,1]>0] # require positive resultant sqt

    #

    data = data[data[:,2]/data[:,1]<max_err]

    #

    if len(data[:,4])<min_taus: # at least min_taus "good" taus

        return None

    return data.T







def plot_datreat(axis, filenames, **kwargs):

    "plot datreat-type file (DrSPINE output)"

    markers     =  itertools.cycle('^vso+*.')

    styles      =  itertools.cycle(['--',':','-.'  ])

    idx   = kwargs.pop('index', None)

    prune = kwargs.pop('prune', None)

    logt  = kwargs.pop('logt', None)

    logs  = kwargs.pop('logs', None)

    #

    for filename in filenames:

        if not os.path.exists(filename):

            continue

        data = read_datreat(filename)

        marker    = next(markers)

        linestyle = next(styles)



        for j, (m, d) in enumerate(data):

            if idx is not None and j not in idx:

                continue

            if prune:

                d = _prune_data(d)

            if d is None:

                continue

            try:

                q    = m['q']

                tau  = d[0]

                sqt  = d[1]

                serr = d[2]

                label="q=%.3f (%s[%s])" % (q, os.path.basename(filename), j)

                axis.errorbar(tau, sqt, yerr=serr, ls=linestyle, marker=marker, label=label)

            except Exception as _exc:

                print(j, _exc)



    if logt:

        axis.set_xscale('log')

    if logs:

        axis.set_yscale('log')

    axis.grid(True)

    axis.legend(loc='best')

pysen/revision.py

+3 −3
Original line number Diff line number Diff line
@@ -2,9 +2,9 @@ 
PySEN revision module

"""

import sys

__version__  = "0.72"

__release__  = "dev4"

__date__     = "Aug 3, 2022"

__version__  = "0.73"

__release__  = "dev1"

__date__     = "Aug 8, 2022"



def version(full=False):

    "get pysen version number"