Commit e53cdf5a authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

scripts/consolidate

parent 6ddfa4eb

scripts/ipynse.py→misc/ipynse.py

+1 −0
Original line number Diff line number Diff line
@@ -2,6 +2,7 @@ 
"""

what is that???

"""

#pylint: disable=skip-file



import sys

import time

scripts/atariplot.py

+3 −1
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ import h5py 
import matplotlib.pyplot as plt





from pysen import ANGSTROM, NANOSECOND

from pysen import ANGSTROM, NANOSECOND, version

from pysen.io import echo_to_hdf

from pysen.atarilib import fit_echo_current, Spectrum
@@ -148,6 +148,8 @@ def main(): 
                        help='set max TOF bin (default=%(default)s)')

    parser.add_argument('--only-echo', '-N', dest='only_echo', action='store_true',   default=False,

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

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

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

    args = parser.parse_args()



    logging.basicConfig(level=args.loglevel, format=r'%(message)s')

scripts/echoplot.py

+4 −11
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ import h5py 
import matplotlib.pyplot as plt



from pysen import ANGSTROM, NANOSECOND, version

from pysen.plotutil import get_nsubplots

from pysen.io import echo_to_hdf

from pysen.atarilib import fit_echo_current, Spectrum
@@ -50,15 +51,7 @@ def echo_plot(hdfile, iecho=0, **kwargs): 
        for echo in list(hdfile['/data'].values()):

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

                ntaus = ntaus + 1

        print(ntaus)

        if ntaus>4:

            nxtau = 4

            nytau = int(np.ceil(ntaus/4))

        else:

            nxtau = 1

            nytau = ntaus

        #print(nxtau, nytau)

        #fig0, axes0 = plt.subplots(nxtau,nytau, figsize=(8,8))

        nxtau, nytau = get_nsubplots(ntaus)

        fig0 = plt.figure(figsize=(8,8))

        fig0.suptitle(r'%s | %s' % (sample, base))
@@ -213,14 +206,14 @@ def main(): 
                        help='set min TOF bin (default=%(default)s)')

    parser.add_argument('--t2',  '-T',  dest='tbin2', type=int,   default=None,

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

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

                        default=False, help='show only center patch')

    parser.add_argument('--verbose', '-v', dest='loglevel', action='store_const',

                        const=logging.DEBUG,  help='verbose output')

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

                        const=logging.WARNING,  help='verbose output')

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

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

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

                        default=False, help='show only center patch')

    args = parser.parse_args()



    if args.loglevel>=logging.INFO:

scripts/genecho.py

+3 −2
Original line number Diff line number Diff line
@@ -11,7 +11,7 @@ import logging 


import numpy as np



from pysen import version, config, ANGSTROM, NANOSECOND

from pysen import version, NANOSECOND

from pysen.io.writer import generate_echo



def resolution(t, lam=6.4, H=0.7):
@@ -109,8 +109,9 @@ def main(): 
            fd = sys.stdin

        else:

            fd = open(args.file)

        #pylint: disable=exec-used

        exec(compile(fd.read(), args.file, 'exec'), glbs)



        #pylint: disable=undefined-variable

        generate_echo(outfile, numor=args.num,

                      sample=sample, detector=detector, physics=physics, taus=taus)

    else:

scripts/mag_field.py

+34 −18
Original line number Diff line number Diff line
@@ -10,21 +10,31 @@ import matplotlib.pyplot as plt 


from pysen import ANGSTROM, NANOSECOND, GAUSS, MICRO, OMEGA_N, version

from pysen.io import echo_to_hdf

from pysen.plotutil import get_nsubplots

#from pysen.atarilib import fit_echo_current, Spectrum





MAX_CHI2_DEFAULT = 1e-2

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

    "plot mag field"

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

    max_chi2 = kwargs.get('max_chi2', 1e-2)

    max_chi2 = kwargs.get('max_chi2', MAX_CHI2_DEFAULT)

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

    #

    a,b  = np.polyfit(t,v0,deg=1)

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

    r    = np.corrcoef(t,v0)

    r    = r[1,0]

    r    = np.cov(t,v0)

    rr   = r[0,0]*r[1,1]

    if rr>0:

        r = r[1,0]/np.sqrt(rr)

    else:

        r = np.nan

    #r    = np.corrcoef(t,v0)

    #r    = r[1,0]

    chi2 = np.sum((v0-v1)**2)

    #maxd = max(abs(v0-v1))

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

    descr2 = r'$\rho$=%.3g $\chi^2$=%.1e' % (r, chi2)

    #descr2 = r'$\rho$=%.3g $\chi^2$=%.1e $(\Delta B)_{max}$=%.3g' % (r, chi2, maxd)

    #

    va   = np.average(v0)

    vd   = max(abs(v0-va))
@@ -33,11 +43,14 @@ def plot_field(ax,t,v,**kwargs): 
    ax.plot(t,v0, '.--', lw=1, label=label)

    ax.plot(t,v1, '-')

    ax.set_ylim(bottom=vmin, top=vmax)

    ax.legend(loc='best')

    ax.text(0.05,0.20,descr1, transform=ax.transAxes, fontsize=7)

    ax.text(0.05,0.10,descr2, transform=ax.transAxes, fontsize=7)

    ax.grid(True, lw=0.5)

    ax.legend(loc='upper left')

    if chi2>max_chi2:

        ax.set_facecolor('yellow')



def plot_magnetic_fields(hdfile, iecho=0):

def plot_magnetic_fields(hdfile, iecho=0, max_chi2=MAX_CHI2_DEFAULT):

    "plot magnetic fields"

    #

    base    = os.path.splitext(os.path.basename(hdfile.filename))[0]
@@ -50,9 +63,9 @@ def plot_magnetic_fields(hdfile, iecho=0): 


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

        if iecho is not None and echo.attrs['id'] != iecho:

            print("skipping  ", echo.name)

            #print("skipping  ", echo.name)

            continue

        print("processing", echo.name)

        #print("processing", echo.name)



        phase   = echo['phase']

        physics = echo['phys']
@@ -70,20 +83,20 @@ def plot_magnetic_fields(hdfile, iecho=0): 
        cur    = phase['phase_current'][:, 0] # actual value

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



        nplots = int(np.ceil(np.sqrt(len(bfield))))

        nxplot, nyplot = get_nsubplots(len(bfield))



        fig, axes = plt.subplots(nplots,nplots, figsize=(9,6))

        fig.subplots_adjust(hspace=0.3, wspace=0.3)

        fig, axes = plt.subplots(nxplot,nyplot, figsize=(9,7))

        fig.subplots_adjust(hspace=0.4, wspace=0.4)

        fig.suptitle(r'%s | %s | $\lambda$=%.2g$\AA$ $Q$=%.3f$\AA^{-1}$ $\tau$=%.3fns' %

                     (sample, base, lam0/ANGSTROM, q0, tau0))



        for iplt, bsensor in enumerate(bfield):

            bmag  = bfield[bsensor]

            label = bsensor.split('.')[-1]

            ax    = axes[iplt//nplots,iplt%nplots]

            plot_field(ax, dj[:nph]/MICRO, bmag[:nph,:]*GAUSS/MICRO, label=label)

        for iplt in range(iplt+1, nplots*nplots):

            ax  = axes[iplt//nplots,iplt%nplots]

            ax    = axes[iplt//nxplot,iplt%nxplot]

            plot_field(ax, dj[:nph]/MICRO, bmag[:nph,:]*GAUSS/MICRO, label=label, max_chi2=max_chi2)

        for iplt in range(iplt+1, nxplot*nyplot):

            ax  = axes[iplt//nxplot,iplt%nxplot]

            ax.axis('off')
@@ -92,10 +105,13 @@ def main(): 
    import argparse



    parser = argparse.ArgumentParser(description='plot magnetic fields')

    parser.set_defaults(loglevel=logging.INFO, outdir='.')

    parser.set_defaults(loglevel=logging.INFO, outdir='.',

                        echo=None, chi2=MAX_CHI2_DEFAULT)

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

    parser.add_argument('--echo',  '-e',  dest='echo', type=int,   default=None,

    parser.add_argument('--echo',  '-e',  dest='echo', type=int,

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

    parser.add_argument('--max-chi2',  '-x',  dest='chi2', type=float,

                        help='set chi2 threshold (default=%(default)s)')

    parser.add_argument('--verbose', '-v', dest='loglevel', action='store_const',

                        const=logging.DEBUG,  help='verbose output')

    parser.add_argument('--quiet', '-q', dest='loglevel', action='store_const',
@@ -121,7 +137,7 @@ def main(): 
        else:

            hfile = filename

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

            plot_magnetic_fields(hdf5file, iecho=args.echo)

            plot_magnetic_fields(hdf5file, iecho=args.echo, max_chi2=args.chi2)

    plt.show()



if __name__ == "__main__":