Commit 86c136a5 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

consistency checks

parent 5fd9462e

pysen/inout/history.py

+6 −1
Original line number Diff line number Diff line
@@ -92,10 +92,15 @@ def list_variables(filenames): 


def extract_data(filenames, names, start_date=None, stop_date=None):

    "extract history data from history.log type files"

    #pylint: disable=too-many-branches

    logger   = logging.getLogger()



    results  = parse_indices(names)

    for filename in tqdm(filenames, colour='green', unit='file', disable=None):

    if tqdm is list:

        filenames = tqdm(filenames)

    else:

        filenames = tqdm(filenames, colour='green', unit='file', disable=None)

    for filename in filenames:

        open_file = get_open_file(filename)

        with open_file(filename) as fd:

            for line in fd.readlines():

pysen/inout/reader.py

+1 −0
Original line number Diff line number Diff line
@@ -812,6 +812,7 @@ def read_transmission(filename): 


def read_diffrun(filename, att_table=None):

    "read nse diffrun file"

    #pylint: disable=too-many-branches

    wavelength  = 0.0

    data_flag   = False

    mon1_flag   = False

pysen/physics/cloizeaux.py

+3 −3
Original line number Diff line number Diff line
@@ -10,8 +10,8 @@ Formulas (19) and (23) 


TODO: implement de Gennes result, Sec.6 and [2]

"""



from numpy import exp, log, pi, sqrt, ceil, vectorize, arange

import numpy as np

from numpy import exp, log, pi, sqrt, vectorize, arange

from numpy import sum as npsum

from numpy.polynomial.laguerre import laggauss

from scipy.integrate import quad
@@ -67,7 +67,7 @@ def fa_kernel(a, y, z): 


def fb_kernel(b, a, y, z):

    "F(b) kernel of [1], see eq.(19)"

    pmax = max(int(ceil(GWIDTH*y/z))+2,2)

    pmax = max(int(np.ceil(GWIDTH*y/z))+2,2)

    #print("DEB: %8d %11.4g %11.4g %11.4g %11.4g " % (pmax,a,b,y,z))

    p  = arange(-pmax, pmax+1)

    u1 = abs((a-2*p)*z)

pysen/plot/nseplot.py

+4 −4
Original line number Diff line number Diff line
@@ -507,7 +507,7 @@ def main(): 


    parser      = argparse.ArgumentParser(description=description)

    parser.set_defaults(loglevel=DEFAULT_LOG_LEVEL)

    subparsers  = parser.add_subparsers(dest='plot', required=True,

    subparsers  = parser.add_subparsers(dest='command', required=True,

                                        help='plot command',

                                        description=None)

    parser.add_argument('--version', '-V', action='version',
@@ -549,7 +549,7 @@ def main(): 
        plt.switch_backend('Agg')



    action = dict(  echo=action_echo, ec=action_echo,

                    atari=action_atari, at=action_atari, summary=action_atari,

                    atari=action_atari, at=action_atari,

                    maps=action_maps,

                    bfield=action_bfield, bf=action_bfield,

                    xyz=action_xyz,
@@ -557,9 +557,9 @@ def main(): 
                    transmission=action_transmission, tr=action_transmission,

                    datreat=action_datreat, dat=action_datreat,

                    qtau=action_qtau, qt=action_qtau,

                    phase_table=action_phase_table, pt=action_phase_table).get(args.plot, None)

                    phase_table=action_phase_table, pt=action_phase_table).get(args.command, None)

    if action is None:

        raise RuntimeError('no action specified for %s' % args.plot)

        raise RuntimeError('no action specified for %s' % args.command)



    kwargs = vars(args)

    action(args.file, **kwargs)

pysen/plot/nseplotlib.py

+22 −37
Original line number Diff line number Diff line
@@ -25,6 +25,15 @@ def _norm_pix(x1, x2, nx, whole_detector=False): 
        return 0, nx

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



def _get_lambda(params):

    "get lambda"

    lmax = []

    try:

        lmax = params['lambdatable']

    except KeyError:

        lmax = params['lambdaTable']

    return np.asarray(lmax).flatten()



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

    "plot mag field"
@@ -175,11 +184,8 @@ def plot_atari(hdfile, iecho=None, **kwargs): 
        #J1       = physics.attrs['prim_fieldintegral']

        phase0   = float(tech.attrs['i5'][0]) or phase_pf

        theta0   = float(tech.attrs['mophi'][0])

        try:

            lmax = params['lambdatable']

        except KeyError:

            lmax = params['lambdaTable']

        lmax  = np.array(lmax).flatten()

        #

        lmax     = _get_lambda(params)

        dlam  = np.ones_like(lmax)*(lmax[1]-lmax[0])

        avlam = lmax - dlam/2.0
@@ -188,10 +194,7 @@ def plot_atari(hdfile, iecho=None, **kwargs): 
        det  = phase['detector'][...]

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

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

        if normalize:

            pcha0 = 1

        else:

            pcha0 = average(pcha)

        pcha0 = 1 if normalize else average(pcha)

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

        #

        edet = sqrt(det)/pcha
@@ -359,20 +362,14 @@ def plot_map(hdfile, iecho=None, **kwargs): 
        itau = itau + 1

        phase   = echo['phase']

        #physics = echo['phys']

        params  = echo['params']

        #params  = echo['params']

        #tech    = echo['tech']



        #tau0    = physics.attrs['fouriertime']/NANOSECOND

        #q0      = physics.attrs['hkl'][0]

        #lam0    = physics.attrs['lambda']

        #phase0  = float(tech.attrs['i5'][0])



        try:

            lmax = params['lambdatable']

        except KeyError:

            lmax = params['lambdaTable']

        lmax = np.array(lmax).flatten()



        #lmax = _get_lambda(params)

        #dlam    = np.ones_like(lmax)*(lmax[1]-lmax[0])



        #phasesens = float(params['phaseangle'].attrs['sensitivities'][0])
@@ -414,11 +411,9 @@ def plot_map(hdfile, iecho=None, **kwargs): 
        elif map_type in ('down',):

            axes.imshow(dn)









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

    "echo plot"

    #pylint: disable=too-many-branches

    #

    center_only     = kwargs.pop('center_only', False)

    only_echo       = kwargs.pop('only_echo', False)
@@ -447,9 +442,7 @@ def plot_echo(hdfile, iecho=None, **kwargs): 
    log = logging.getLogger()

    #

    center_only = center_only or resolution_plot



    base    = os.path.splitext(os.path.basename(hdfile.filename))[0]



    comment = hdfile.attrs['master_comment']

    #comment = comment.decode("utf-8")

    sample  = comment.split()[0]
@@ -493,20 +486,12 @@ def plot_echo(hdfile, iecho=None, **kwargs): 
        params  = echo['params']

        tech    = echo['tech']





        tau0    = physics.attrs['fouriertime']/NANOSECOND

        q0      = physics.attrs['hkl'][0]

        lam0    = physics.attrs['lambda']

        phase0  = float(tech.attrs['i5'][0])



        try:

            lmax = params['lambdatable']

        except KeyError:

            lmax = params['lambdaTable']

        lmax = np.array(lmax).flatten()



        lmax    = _get_lambda(params)

        dlam    = np.ones_like(lmax)*(lmax[1]-lmax[0])



        phasesens = float(params['phaseangle'].attrs['sensitivities'][0])



        det  = phase['detector'][...]
@@ -552,10 +537,12 @@ def plot_echo(hdfile, iecho=None, **kwargs): 
            ax.grid()

            if nytau>1 and (itau%nytau)!=1:

                ax.set_yticklabels([])

            if max(y)>maxy:

                maxy = max(y)

            if min(y)<miny:

                miny = min(y)

            miny = min(miny, min(y))

            maxy = max(maxy, max(y))

            #if max(y)>maxy:

            #    maxy = max(y)

            #if min(y)<miny:

            #    miny = min(y)

            continue



        npx, nx, ny, nt = det.shape
@@ -565,7 +552,6 @@ def plot_echo(hdfile, iecho=None, **kwargs): 
        pha = pha.sum(axis=(2, 4)) # pixel rebin

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





        fig, axes = plt.subplots(nxx,nyy, figsize=(8,8))

        fig.subplots_adjust(hspace=0.05, wspace=0.05)
@@ -583,7 +569,6 @@ def plot_echo(hdfile, iecho=None, **kwargs): 
                dn = y[nph:n_idx['up']]

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

                #



                upave = average(up)

                dnave = average(dn)

                udave = (upave+dnave)/2