Commit 1f0a80db authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

ver 1.0-rc1

parent d6b65567

pysen/echo/reduce.py

+9 −3
Original line number Diff line number Diff line
@@ -12,11 +12,17 @@ def get_symmetry_phase(hdfile, iecho=None, **kwargs): 
    "get the symmetry phase (for phase tables)"

    #

    tbin1   = kwargs.pop('tbin1', 0)

    tbin2   = kwargs.pop('tbin2',-1)

    tbin2   = kwargs.pop('tbin2', None)

    xpix1   = kwargs.pop('xpix1', 0)

    xpix2   = kwargs.pop('xpix2',-1)

    xpix2   = kwargs.pop('xpix2', None)

    ypix1   = kwargs.pop('ypix1', 0)

    ypix2   = kwargs.pop('ypix2',-1)

    ypix2   = kwargs.pop('ypix2', None)



    if kwargs.get('center_only'):

        tbin1, tbin2 = 4, -4

        xpix1, xpix2 = 5, -5

        ypix1, ypix2 = 5, -5





    log = logging.getLogger()

pysen/plot/nseplot.py

+37 −20
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ from pysen.plot import ( plot_echo, plot_atari, plot_map, 
def action_default(filenames, **kwargs):

    "default action for echo, atari, etc"

    action  = kwargs.pop('action')

    tau     = kwargs.pop('tau')

    taus    = kwargs.pop('taus')

    outdir  = kwargs.pop('outdir')

    savefig = kwargs.pop('savefig')

    log = logging.getLogger()
@@ -37,7 +37,7 @@ def action_default(filenames, **kwargs): 
            if ext != ".h5":

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

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

                action(hdf5file, tau, **kwargs)

                action(hdf5file, taus, **kwargs)

            if savefig:

                plt.savefig(basename+'-'+savefig)

        except (OSError,KeyError,RuntimeError) as exc:
@@ -246,7 +246,7 @@ def arguments_selection_tof(): 
def arguments_selection_pix():

    """pixel selection arguments"""

    pars = argparse.ArgumentParser(add_help=False)

    pars.set_defaults(xpix1=10,xpix2=22,ypix1=10,ypix2=22, whole_detector=False)

    pars.set_defaults(xpix1=10,xpix2=-10,ypix1=10,ypix2=-10, whole_detector=False)

    grp  = pars.add_argument_group('options to select pixels')

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

                     help='set min X pix (default=%(default)s)')
@@ -281,10 +281,14 @@ def add_echo_options(subparser, parents=None): 
    pars = subparser.add_parser('echo', parents=parents,

                      help='plot echo (.echo or .h5 files)',

                      description='create echo plot(s)')

    pars.set_defaults(center_only=False, resolution_plot=False, absy=0, npix=4, tau=0)

    pars.set_defaults(center_only=False, resolution_plot=False, absy=0, npix=4, taus=None)

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

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

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

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

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

                        help='select list of taus')

    except ValueError:

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

                        help='select list of taus')

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

                       help='show only center patch')

    pars.add_argument('--only-echo', dest='only_echo', action='store_true',
@@ -304,8 +308,12 @@ def add_atari_options(subparser, parents=None): 
                      help='atari plot (.echo or .h5 files)',

                      description='create atari plot(s)')

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

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

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

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

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

                        help='select list of taus')

    except ValueError:

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

                        help='select list of taus')

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

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

    pars.add_argument('--incoherent', '-I', dest='incoherent', action='store_true',
@@ -389,8 +397,12 @@ def add_plotmap_options(subparser, parents=None): 
                      help='map',

                      description='create map plots')

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

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

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

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

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

                        help='select list of taus')

    except ValueError:

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

                        help='select list of taus')

    pars.add_argument('--map-type', dest='map_type', choices=['all', 'up', 'down'],

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

    pars.add_argument('--num-pix', '-N', dest='npix', type=int,
@@ -402,9 +414,13 @@ def add_bfield_options(subparser, parents=None): 
                      help='bfield',

                      description='create bfield plots')

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

    pars.set_defaults(tau=None,max_chi2=1e-2, axis=-1)

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

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

    pars.set_defaults(max_chi2=1e-2, axis=-1)

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

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

                        help='select list of taus')

    except ValueError:

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

                        help='select list of taus')

    pars.add_argument('--max-chi2', dest='max_chi2', type=float,

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

    pars.add_argument('--axis', dest='axis', type=int,
@@ -429,17 +445,16 @@ def add_qtau_options(subparser, parents=None): 
    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',

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

                        help='select list of taus')

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

        pars.add_argument('--tbin', dest='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',

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

                        help='select list of taus')

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

        pars.add_argument('--tbin', dest='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')

    grp.add_argument('--full', '-F', dest='full', action='store_true',
@@ -459,9 +474,8 @@ def add_ptab_options(subparser, parents=None): 
    "make phase table"

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

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

    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)')
@@ -470,6 +484,9 @@ def add_ptab_options(subparser, parents=None): 
    pars.add_argument('--threshold', dest='threshold', metavar='thres', type=float,

                     help=argparse.SUPPRESS)

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

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

                       help='show only center patch')





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

# the main command line interface

pysen/plot/nseplotlib.py

+66 −59
Original line number Diff line number Diff line
@@ -6,6 +6,8 @@ import logging 


import numpy as np

import matplotlib.pyplot as plt



from numpy import sqrt, radians, average, mod, polyval

from  matplotlib import colors



from .. import (ANGSTROM, NANOSECOND, GAUSS, MICRO, OMEGA_N, config, get_q)
@@ -14,23 +16,30 @@ from ..mathutil import linear_fit 
from .plotutil import get_nsubplots

from .echo     import plot_single_echo





MAX_CHI2_DEFAULT_BFIELD = 1e-2 # TODO: explain the meaning of this



def norm_pix(x1, x2, nx, whole_detector=False):

    "normalize pixel"

    if whole_detector:

        return 0, nx

    return mod(x1,nx), mod(x2,nx)



def plot_field(ax,t,v,**kwargs):

    "plot mag field"



    axis     = kwargs.get('axis', -1)

    label    = kwargs.get('label'  , '')

    max_chi2 = kwargs.get('max_chi2', MAX_CHI2_DEFAULT_BFIELD)

    v0 = np.sqrt(np.sum(v**2,axis=-1))

    v0 = sqrt(sum(v**2,axis=-1))

    if axis>0:

        v0 = v[:,axis-1]

        label = "%s (%s)" % (label,{1:'x',2:'y',3:'z'}.get(axis,''))

    a, b, chi2, corr, maxd = linear_fit(t, v0)

    v1   = np.polyval([a,b],t)

    v1   = polyval([a,b],t)

    descr1 = r'a=%.2e b=%.3g' % (a,b)

    descr2 = r'$\rho$=%.3g $\chi^2$=%.1e' % (corr, chi2) # pylint: disable=bad-string-format-type

    va   = np.average((max(v0), min(v0)))

    va   = average((max(v0), min(v0)))

    vd   = max(abs(v0-va))

    vmin = va-max(vd,1.5)

    vmax = va+max(vd,1.5)
@@ -49,7 +58,7 @@ def plot_field(ax,t,v,**kwargs): 
    return ok, dict(chi2=chi2, maxd=maxd, corr=corr, slope=a, offset=b)





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

def plot_magnetic_fields(hdfile, iecho=None, **kwargs):

    "plot magnetic fields"

    #

    axis     = kwargs.get('axis', -1)
@@ -66,7 +75,7 @@ def plot_magnetic_fields(hdfile, iecho=0, **kwargs): 
    nph     = hdfile['/'].attrs['point_to_down']



    for echo in list(hdfile['/data'].values()):

        if iecho and echo.attrs['id'] != iecho:

        if not (iecho is None or echo.attrs['id'] in iecho):

            continue



        phase   = echo['phase']
@@ -83,7 +92,7 @@ def plot_magnetic_fields(hdfile, iecho=0, **kwargs): 


        bfield = phase['bfield']

        cur    = phase['phase_current'][:, 0] # actual value

        dj     = np.radians(phasesens*(cur-cur0))/OMEGA_N/lam0

        dj     = radians(phasesens*(cur-cur0))/OMEGA_N/lam0



        nxplot, nyplot = get_nsubplots(len(bfield))
@@ -112,7 +121,7 @@ def plot_magnetic_fields(hdfile, iecho=0, **kwargs): 
            ax  = axes[iplt//nxplot,iplt%nxplot]

            ax.axis('off')



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

def plot_atari(hdfile, iecho=None, **kwargs):

    "atari plot"

    #

    tbin1   = kwargs.pop('tbin1',0)      # TOF bins
@@ -147,12 +156,11 @@ def plot_atari(hdfile, iecho=0, **kwargs): 
    nph     = n_idx['dn']

    comment = hdfile.attrs['master_comment']



    if whole_detector:

        xpix1, xpix2 = 0, nx

        ypix1, ypix2 = 0, ny

    xpix1, xpix2 = norm_pix(xpix1, xpix2, nx, whole_detector)

    ypix1, ypix2 = norm_pix(ypix1, ypix2, ny, whole_detector)



    for echo in list(hdfile['/data'].values()):

        if iecho and echo.attrs['id'] != iecho:

        if not (iecho is None or echo.attrs['id'] in iecho):

            continue



        phase   = echo['phase']
@@ -183,25 +191,25 @@ def plot_atari(hdfile, iecho=0, **kwargs): 
        if normalize:

            pcha0 = 1

        else:

            pcha0 = np.average(pcha)

            pcha0 = average(pcha)

        pcha = pcha[:,np.newaxis,np.newaxis,np.newaxis]/float(pcha0)

        #

        edet = np.sqrt(det)/pcha

        edet = sqrt(det)/pcha

        det  = det/pcha

        wlen = np.sum(det, axis=(0,1,2)) # all but TOF axis

        wlen = sum(det, axis=(0,1,2)) # all but TOF axis

        #



        YY, XX, TT = np.mgrid[ypix1:ypix2, xpix1:xpix2, tbin1:tbin2 or nt]

        theta, _ = config.pixel_angle(XX, YY, np.radians(theta0)) # theta,phi

        theta, _ = config.pixel_angle(XX, YY, radians(theta0)) # theta,phi

        alam     = avlam[TT]

        q_pix    = get_q(alam, theta)*ANGSTROM

        tau_pix   = (alam/lam0)**3*tau0



        flux = np.tile(wlen[tbin1:tbin2], q_pix.shape[:-1]).reshape(q_pix.shape)

        qave = np.average(q_pix, weights=flux)

        qvar = np.sqrt(np.average((q_pix-qave)**2, weights=flux))

        tave = np.average(tau_pix, weights=flux)

        tvar = np.sqrt(np.average((tau_pix-tave)**2, weights=flux))

        qave = average(q_pix, weights=flux)

        qvar = sqrt(average((q_pix-qave)**2, weights=flux))

        tave = average(tau_pix, weights=flux)

        tvar = sqrt(average((tau_pix-tave)**2, weights=flux))



        #

        fig, axes = plt.subplots(2,2,figsize=(10,8))
@@ -213,7 +221,7 @@ def plot_atari(hdfile, iecho=0, **kwargs): 
        ax.grid(True)



        ax = axes[0,1]

        xatari = np.sum(det, axis=(1,2)).T

        xatari = sum(det, axis=(1,2)).T

        extent = (cur[0], cur[nph-1])

        if tbin2 is None:

            extent = extent + (lmax[tbin1]/ANGSTROM, max(lmax)/ANGSTROM)
@@ -224,7 +232,7 @@ def plot_atari(hdfile, iecho=0, **kwargs): 
        ax.imshow(xatari, origin='lower', extent=extent, aspect='auto')



        ax = axes[1,0]

        img = np.sum(det[:,:,:,tbin1:tbin2], axis=(0,-1))

        img = sum(det[:,:,:,tbin1:tbin2], axis=(0,-1))

        if logz:

            norm = colors.LogNorm(max(1,vmin), vmax)

            im = ax.imshow(img , aspect='equal', norm=norm)
@@ -243,13 +251,13 @@ def plot_atari(hdfile, iecho=0, **kwargs): 
        ax = axes[1,1]

        pha  = det [:,ypix1:ypix2,xpix1:xpix2,tbin1:tbin2]

        epha = edet[:,ypix1:ypix2,xpix1:xpix2,tbin1:tbin2]

        wlen = np.sum(pha, axis=(0,1,2)) # all but TOF axis

        wlen = sum(pha, axis=(0,1,2)) # all but TOF axis



        dn   = np.sum(pha[nph:n_idx['up']], axis=(1,2,3))

        up   = np.sum(pha[n_idx['up']:], axis=(1,2,3))

        #epha = np.sqrt(np.sum(pha[:nph], axis=(1,2,3)))

        epha = np.sqrt(np.sum(epha[:nph]**2, axis=(1,2,3)))

        pha  = np.sum(pha[:nph], axis=(1,2,3))

        dn   = sum(pha[nph:n_idx['up']], axis=(1,2,3))

        up   = sum(pha[n_idx['up']:], axis=(1,2,3))

        #epha = sqrt(sum(pha[:nph], axis=(1,2,3)))

        epha = sqrt(sum(epha[:nph]**2, axis=(1,2,3)))

        pha  = sum(pha[:nph], axis=(1,2,3))



        spectrum =  Spectrum(lam=lmax[tbin1:tbin2], dlam=dlam[tbin1:tbin2], flux=wlen)# [tbin1:tbin2])

        (phase_ef, phase_err), (xef, yef), res = fit_echo_current(cur[:nph], (pha, epha), spectrum, global_fit=phase_pf is None,
@@ -271,16 +279,16 @@ def plot_atari(hdfile, iecho=0, **kwargs): 
            _txt = r'$A(Q,t)$=%.3g$\pm$%.3g' % res['amplitude']

        else:

            minup = 0

            maxup = np.max((np.max(up), np.max(dn)))*1.2

            res['up'] = np.average(up),np.sqrt(np.sum(up)/len(up))

            res['dn'] = np.average(dn),np.sqrt(np.sum(dn)/len(dn))

            maxup = max((max(up), max(dn)))*1.2

            res['up'] = average(up),sqrt(sum(up)/len(up))

            res['dn'] = average(dn),sqrt(sum(dn)/len(dn))

            R  = 2*res['amplitude'][0]/( res['up'][0] - res['dn'][0] )

            eR = R * res['amplitude'][1]/res['amplitude'][0]

            ax.errorbar(cur[nph:n_idx['up']], dn, fmt='.', color=dcol)

            ax.errorbar(cur[n_idx['up']:],    up, fmt='.', color=dcol)

            _txt = r'$R(Q,t)$=%.3g$\pm$%.3g' % (R,eR)

            ax.axhline(np.average(up))

            ax.axhline(np.average(dn))

            ax.axhline(average(up))

            ax.axhline(average(dn))

            log.info("R=%.4g(%.4g) Phase=%.4g(%.4g) Amp=%.4g(%.4g) Up=%.4g(%.4g) Down=%.4g(%.4g)",

                R, eR,

                phase_ef, phase_err,
@@ -315,7 +323,7 @@ def plot_atari(hdfile, iecho=0, **kwargs): 
        fig.suptitle(r'%s: %s $Q$=%.3f$\AA^{-1}$ $\tau$=%.3gns' % (base, comment, q0,tau0))





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

def plot_map(hdfile, iecho=None, **kwargs):

    "map plot"

    #

    npix    = kwargs.pop('npix',None) or 4    # pix
@@ -345,7 +353,7 @@ def plot_map(hdfile, iecho=0, **kwargs): 


    itau = 0

    for echo in list(hdfile['/data'].values()):

        if iecho and echo.attrs['id'] != iecho:

        if not (iecho is None or echo.attrs['id'] in iecho):

            continue



        itau = itau + 1
@@ -372,10 +380,10 @@ def plot_map(hdfile, iecho=0, **kwargs): 
        det  = phase['detector'][...]

        pcha = phase['proton_charge'][...]

        #cur  = phase['phase_current'][:, 0] # actual value

        pcha0 = np.average(pcha)

        pcha0 = average(pcha)

        pcha = pcha[:,np.newaxis,np.newaxis,np.newaxis]/float(pcha0)

        det  = det/pcha

        #wlen = np.sum(det, axis=(0,1,2))

        #wlen = sum(det, axis=(0,1,2))



        #spectrum =  Spectrum(lam=lmax, dlam=dlam, flux=wlen)

        #spectrum =  Spectrum(lam=lmax[tbin1:tbin2], dlam=dlam[tbin1:tbin2], flux=wlen[tbin1:tbin2])
@@ -387,14 +395,14 @@ def plot_map(hdfile, iecho=0, **kwargs): 
        nxx = nx//npix

        pha = det.reshape(npx, nyy, npix, nxx, npix, nt)

        pha = pha.sum(axis=(2, 4)) # pixel rebin

        pha = np.sum(pha[:,:,:,tbin1:tbin2],axis=-1) # tof summation

        pha = sum(pha[:,:,:,tbin1:tbin2],axis=-1) # tof summation





        dn  = np.average(pha[nph:n_idx['up'],:,:], axis=0)

        up  = np.average(pha[n_idx['up']:   ,:,:], axis=0)

        dn  = average(pha[nph:n_idx['up'],:,:], axis=0)

        up  = average(pha[n_idx['up']:   ,:,:], axis=0)



        #y  = np.sum(det[:,ypix1:ypix2,xpix1:xpix2,tbin1:tbin2], axis=(1,2,3))

        #ey = np.sqrt(y)

        #y  = sum(det[:,ypix1:ypix2,xpix1:xpix2,tbin1:tbin2], axis=(1,2,3))

        #ey = sqrt(y)

        #(phase_ef0,_) , (xef,yef), res = fit_echo_current(cur[:nph], (y[:nph], ey[:nph]), spectrum,

        #                                             lam0=lam0, phase0=phase0, phasesens=phasesens,

        #                                             incoherent=incoherent)
@@ -409,7 +417,7 @@ def plot_map(hdfile, iecho=0, **kwargs): 






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

def plot_echo(hdfile, iecho=None, **kwargs):

    "echo plot"

    #

    center_only     = kwargs.pop('center_only', False)
@@ -457,15 +465,14 @@ def plot_echo(hdfile, iecho=0, **kwargs): 
    nph     = n_idx['dn']

    miny, maxy    = np.inf, 0



    if whole_detector:

        xpix1, xpix2 = 0, nx

        ypix1, ypix2 = 0, ny

    xpix1, xpix2 = norm_pix(xpix1, xpix2, nx, whole_detector)

    ypix1, ypix2 = norm_pix(ypix1, ypix2, nx, whole_detector)



    if  center_only:

        ntaus = 0

        if not resolution_plot:

            for echo in list(hdfile['/data'].values()):

                if not iecho or echo.attrs['id'] == iecho:

                if iecho is None or echo.attrs['id'] in iecho:

                    ntaus = ntaus + 1

        if ntaus>1 or resolution_plot:

            ntaus = ntaus + 1 # resolution curve
@@ -476,7 +483,7 @@ def plot_echo(hdfile, iecho=0, **kwargs): 
    itau = 0

    resolution = []

    for echo in list(hdfile['/data'].values()):

        if iecho and echo.attrs['id'] != iecho:

        if not (iecho is None or echo.attrs['id'] in iecho):

            continue



        itau = itau + 1
@@ -505,16 +512,16 @@ def plot_echo(hdfile, iecho=0, **kwargs): 
        det  = phase['detector'][...]

        pcha = phase['proton_charge'][...]

        cur  = phase['phase_current'][:, 0] # actual value

        pcha0 = np.average(pcha)

        pcha0 = average(pcha)

        pcha = pcha[:,np.newaxis,np.newaxis,np.newaxis]/float(pcha0)

        det  = det/pcha

        wlen = np.sum(det, axis=(0,1,2))

        wlen = sum(det, axis=(0,1,2))



        #spectrum =  Spectrum(lam=lmax, dlam=dlam, flux=wlen)

        spectrum =  Spectrum(lam=lmax[tbin1:tbin2], dlam=dlam[tbin1:tbin2], flux=wlen[tbin1:tbin2])



        y  = np.sum(det[:,ypix1:ypix2,xpix1:xpix2,tbin1:tbin2], axis=(1,2,3))

        ey = np.sqrt(y)

        y  = sum(det[:,ypix1:ypix2,xpix1:xpix2,tbin1:tbin2], axis=(1,2,3))

        ey = sqrt(y)

        dn = y[nph:n_idx['up']]

        up = y[n_idx['up']:]

        _ = fit_echo_current(cur[:nph], (y[:nph], ey[:nph]), spectrum,
@@ -524,8 +531,8 @@ def plot_echo(hdfile, iecho=0, **kwargs): 
        if center_only:

            res['current0'] = (phase_ef0, phase_err)

            if not only_echo:

                res['up'] = np.average(up), np.sqrt(np.sum(up)/len(up))

                res['dn'] = np.average(dn), np.sqrt(np.sum(dn)/len(dn))

                res['up'] = average(up), sqrt(sum(up)/len(up))

                res['dn'] = average(dn), sqrt(sum(dn)/len(dn))

                R = 2*res['amplitude'][0]/( res['up'][0] - res['dn'][0] )

                resolution.append((tau0, R))

                log.info("tau={0:.3g}ns R={1:.3g}".format(tau0,R))
@@ -556,7 +563,7 @@ def plot_echo(hdfile, iecho=0, **kwargs): 
        nxx = nx//npix

        pha = det.reshape(npx, nyy, npix, nxx, npix, nt)

        pha = pha.sum(axis=(2, 4)) # pixel rebin

        pha = np.sum(pha[:,:,:,tbin1:tbin2],axis=-1) # tof summation

        pha = sum(pha[:,:,:,tbin1:tbin2],axis=-1) # tof summation





        fig, axes = plt.subplots(nxx,nyy, figsize=(8,8))
@@ -577,10 +584,10 @@ def plot_echo(hdfile, iecho=0, **kwargs): 
                up = y[n_idx['up']:]

                #



                upave = np.average(up)

                dnave = np.average(dn)

                upave = average(up)

                dnave = average(dn)

                udave = (upave+dnave)/2

                ave   = np.average(y[:nph])

                ave   = average(y[:nph])

                #std   = np.std(y[:nph])



                if udave<min_counts or ave<min_counts:
@@ -601,8 +608,8 @@ def plot_echo(hdfile, iecho=0, **kwargs): 
                    #if abs(R)<min_amp:

                    #    continue



                    res['up'] = upave, np.sqrt(np.sum(up)/len(up))

                    res['dn'] = dnave, np.sqrt(np.sum(dn)/len(dn))

                    res['up'] = upave, sqrt(sum(up)/len(up))

                    res['dn'] = dnave, sqrt(sum(dn)/len(dn))

                    res['current0'] = (phase_ef, phase_err)

                    plot_single_echo(ax, (cur, y, ey), (nph,n_idx['up']), fit=(xef, yef),

                                     res=res, label='(%s,%s)' % (i,j), only_echo=only_echo,

pysen/revision.py

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

"""

import sys

__version__  = "0.76"

__release__  = "dev2"

__date__     = "Aug 19, 2022"

__version__  = "1.0"

__release__  = "rc1"

__date__     = "Aug 22, 2022"



def version(full=False):

    "get pysen version number"

scripts/pysen_completion

+1 −1
Original line number Diff line number Diff line
@@ -63,7 +63,7 @@ else 
fi





#complete -o filenames -F _pysen_completions nseplot

complete -o filenames -F _pysen_completions nseplot



# vim: filetype=bash