Commit a7579e82 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

added xyz analysis to nseplot

parent 7f194315

pysen/plot/nseplot.py

+80 −67
Original line number Diff line number Diff line
@@ -4,15 +4,18 @@ 
import os.path

import argparse



import numpy as np

import h5py

import matplotlib.pyplot as plt



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_magnetic_fields,

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

                           plot_xyz,

                           plot_magnetic_fields,

                           plot_diffrun, plot_transmission )

from pysen.plot.cmdline import NsePlotApp

#from pysen.plot.cmdline import NsePlotApp



def action_default(filenames, **kwargs):

    "default action for echo, atari, etc"
@@ -39,6 +42,26 @@ def action_default(filenames, **kwargs): 
            print(exc)

    return to_show



def action_xyz(filenames, **kwargs):

    "default action for xyz"

    outdir  = kwargs.pop('outdir')

    savefig = kwargs.pop('savefig')

    overwrite = kwargs.pop('overwrite')

    log = kwargs.pop('log')

    hfiles = []

    for filename in filenames:

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

        if ext==".dat":

            hfiles.append(convert_to_hdf(filename, outdir, data_type='magnetic', overwrite=overwrite))

        else:

            hfiles.append(filename)

    plot_xyz(*hfiles, **kwargs)



    if not savefig:

        to_show = True

    return to_show





def action_diffrun(filenames, **kwargs):

    "action for diffrun"

    savefig = kwargs.pop('savefig')
@@ -97,25 +120,35 @@ def arguments_selection(pars, pix=True, tof=True): 
        pars.add_argument('--whole-detector', '-W', dest='whole_detector', action='store_true',

                          help='show sum over entire detector area')



def arguments_vertscale(pars):

    """vertical scale arguments"""

    pars.add_argument('--vmin' , dest='vmin', type=int,

                        help='set min vertical scale (default=%(default)s)')

    pars.add_argument('--vmax' , dest='vmax', type=int,

                        help='set max vertical scale (default=%(default)s)')

    pars.add_argument('--logz' , dest='logz', action='store_true',

                           help='detector image log vertical scale')

    pars.add_argument('--normalize', '-n' , dest='normalize', action='store_true',

                           help='normalize results')



def main():

    "the main"



    plot_action = dict(echo=plot_echo, atari=plot_atari, maps=plot_map, bfield=plot_magnetic_fields, diffrun=plot_diffrun)

    description = "SNS NSE plotting tool"



    parser_top  = argparse.ArgumentParser(description=description)

    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=False, help='what to plot')

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



    # common arguments

    parser = argparse.ArgumentParser(add_help=False)

    parser.set_defaults(loglevel=1, outdir='.', tbin1=0, tbin2=None,

                        vmin=0, vmax=None, logz=False,

    parser.set_defaults(loglevel=1, outdir='.', 

                        tau=0, npix=0,

                        absy=0, normalize=False,

                        tbin1=0, tbin2=None,

                        xpix1=10,xpix2=22,ypix1=10,ypix2=22,

                        vmin=0, vmax=None, logz=False, normalize=False, absy=0, 

                        center_only=False, whole_detector=False,

                        map_type='all', phase0=None,

                        incoherent=False, max_chi2=1e3)
@@ -151,20 +184,6 @@ def main(): 
    grp_echo.add_argument('--num-pix', '-N', dest='npix', metavar='N', type=int,

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

    arguments_selection(grp_echo)

    #grp_echo.add_argument('--t1' , '-b',  dest='tbin1', type=int,

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

    #grp_echo.add_argument('--t2' , '-B',  dest='tbin2', type=int,

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

    #grp_echo.add_argument('--x1' , dest='xpix1', type=int,

    #                      help='set min X pix (default=%(default)s)')

    #grp_echo.add_argument('--x2' , dest='xpix2', type=int,

    #                      help='set max X pix (default=%(default)s)')

    #grp_echo.add_argument('--y1' , dest='ypix1', type=int,

    #                      help='set min Y pix (default=%(default)s)')

    #grp_echo.add_argument('--y2' , dest='ypix2', type=int,

    #                      help='set max Y pix (default=%(default)s)')

    #grp_echo.add_argument('--whole-detector', '-W', dest='whole_detector', action='store_true',

    #                      help='show sum over entire detector area')

    grp_echo.add_argument('--resolution', '-R', dest='resolution_plot', action='store_true',

                          help='TBD')

    # atari plot
@@ -172,55 +191,28 @@ def main(): 
    grp_atari = parser_atari.add_argument_group('atari plot options')

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

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

    arguments_selection(grp_atari)

    arguments_vertscale(grp_atari)

    grp_atari.add_argument('--only-echo', dest='only_echo', action='store_true',

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

    grp_atari.add_argument('--incoherent', '-I', dest='incoherent', action='store_true',

                          help='treat data as from incoherent scatterer')

    arguments_selection(grp_atari)

    #grp_atari.add_argument('--t1' , '-b',  dest='tbin1', type=int,

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

    #grp_atari.add_argument('--t2' , '-B',  dest='tbin2', type=int,

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

    #grp_atari.add_argument('--x1' , dest='xpix1', type=int,

    #                       help='set min X pix (default=%(default)s)')

    #grp_atari.add_argument('--x2' , dest='xpix2', type=int,

    #                       help='set max X pix (default=%(default)s)')

    #grp_atari.add_argument('--y1' , dest='ypix1', type=int,

    #                       help='set min Y pix (default=%(default)s)')

    #grp_atari.add_argument('--y2' , dest='ypix2', type=int,

    #                       help='set max Y pix (default=%(default)s)')

    #grp_atari.add_argument('--whole-detector', '-W', dest='whole_detector', action='store_true',

    #                       help='select the entire detector area')

    grp_atari.add_argument('--vmin' , dest='vmin', type=float,

                           help='detector image min vertical scale (default=%(default)s) ')

    grp_atari.add_argument('--vmax' , dest='vmax', type=float,

                           help='detector image max vertical scale (default=%(default)s)')

    grp_atari.add_argument('--logz' , dest='logz', action='store_true',

                           help='detector image log vertical scale')

    grp_atari.add_argument('--normalize', '-n' , dest='normalize', action='store_true',

                            help='normalize results to proton charge')

    grp_atari.add_argument('--phase0' , dest='phase0', type=float,

                           help='set inital phase for echo fitting (default=%(default)s)')



    # 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_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'],

                         help='(default: %(default)s)')

    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_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,

                            help='set max chi-square (default=%(default)s)')

    grp_bfield.add_argument('--axis', dest='axis', type=int, default=-1,

                            help='set axis to plot  (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.set_defaults(overwrite=False, qmin=0, qmax=np.inf, deltaq=0.001)

    arguments_selection(grp_xyz)

    arguments_vertscale(grp_xyz)

    grp_xyz.add_argument('--qmin', dest='qmin', type=float,

                           help='qmin (default=%(default)s)')

    grp_xyz.add_argument('--qmax', dest='qmax', type=float,

                           help='qmax (default=%(default)s)')

    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')
@@ -262,14 +254,33 @@ def main(): 
    grp_trans.add_argument('--echodet', '-e', dest='echodet', action='store_true',

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



    # 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_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'],

                         help='(default: %(default)s)')

    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_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,

                            help='set max chi-square (default=%(default)s)')

    grp_bfield.add_argument('--axis', dest='axis', type=int, default=-1,

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



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

    args = parser_top.parse_args()

    log = setup_logger(args.loglevel)

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



    if not args.what:

        NsePlotApp().cmdloop()

        return

    #if not args.what:

    #    NsePlotApp().cmdloop()

    #    return

        



    plt.rcParams.update({'figure.max_open_warning': 0})
@@ -278,9 +289,11 @@ def main(): 


    kwargs = vars(args)



    plot_action = dict(echo=plot_echo, atari=plot_atari, maps=plot_map, bfield=plot_magnetic_fields, diffrun=plot_diffrun)

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

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

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

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

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

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

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

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

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

pysen/plot/xyz_analysis.py

deleted100755 → 0
+0 −81
Original line number Diff line number Diff line 
#!/usr/bin/env python

"xyz analysis script"



import os.path

import argparse



import numpy as np

import matplotlib.pyplot as plt



from pysen       import version

from pysen.inout import convert_to_hdf

from pysen.plot  import plot_xyz



def main():

    "the main"



    description = "SNS-NSE xyz analysis tool"

    parser = argparse.ArgumentParser(description=description)

    parser.set_defaults(outdir='.', overwrite=False,

                        tbin1=0, tbin2=None, normalize=False,

                        xpix1=10,xpix2=22,ypix1=10,ypix2=22,

                        vmin=0, vmax=None, logz=False,

                        qmin=0, qmax=np.inf, deltaq=0.001)

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

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

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

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

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

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

                        help='save data to a csv file')

    parser.add_argument('--t1' , '-b',  dest='tbin1', type=int,

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

    parser.add_argument('--t2' , '-B',  dest='tbin2', type=int,

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

    parser.add_argument('--x1' , dest='xpix1', type=int,

                        help='set min X pix (default=%(default)s)')

    parser.add_argument('--x2' , dest='xpix2', type=int,

                        help='set max X pix (default=%(default)s)')

    parser.add_argument('--y1' , dest='ypix1', type=int,

                        help='set min Y pix (default=%(default)s)')

    parser.add_argument('--y2' , dest='ypix2', type=int,

                        help='set max Y pix (default=%(default)s)')

    parser.add_argument('--whole-detector', '-W', dest='whole_detector', action='store_true',

                          help='select the entire detector area')

    parser.add_argument('--qmin', dest='qmin', type=float,

                           help='qmin (default=%(default)s)')

    parser.add_argument('--qmax', dest='qmax', type=float,

                           help='qmax (default=%(default)s)')

    parser.add_argument('--vmin' , dest='vmin', type=int,

                        help='set min vertical scale (default=%(default)s)')

    parser.add_argument('--vmax' , dest='vmax', type=int,

                        help='set max vertical scale (default=%(default)s)')

    parser.add_argument('--logz' , dest='logz', action='store_true',

                           help='detector image log vertical scale')

    parser.add_argument('--normalize', '-n' , dest='normalize', action='store_true',

                           help='normalize results to proton charge')

    parser.add_argument('--delta-q', dest='deltaq', type=float,

                           help='q histogram bin witdth')



    args = parser.parse_args()



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





    if args.savefig:

        plt.switch_backend('Agg')

    hfiles = []

    for filename in args.file:

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

        if ext==".dat":

            hfiles.append(convert_to_hdf(filename, args.outdir, data_type='magnetic', overwrite=args.overwrite))

        else:

            hfiles.append(filename)

    kwargs  = vars(args)

    plot_xyz(*hfiles, **kwargs)



    if not args.savefig:

        plt.show()



if __name__ == "__main__":

    main()

pysen/revision.py

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

import sys

__version__  = "0.72"

__release__  = "dev3"

__release__  = "dev4"

__date__     = "Aug 3, 2022"



def version(full=False):

setup.py

+2 −3
Original line number Diff line number Diff line
@@ -24,13 +24,12 @@ setup( 
        'console_scripts': [

            'convert2hdf      = pysen.inout.convert2hdf:main',

            'make_phase_table = pysen.plot.make_phase_table:main',

            'xyz_analysis     = pysen.plot.xyz_analysis:main',

            'nseplot          = pysen.plot.nseplot:main',

        ]

      },

      scripts       = [

        'scripts/plot_diffrun.py',

        'scripts/plot_transmission.py',

        #'scripts/plot_diffrun.py',

        #'scripts/plot_transmission.py',

        # to move

        'scripts/plot_dtrfile.py',

        'scripts/qtau.py',