Commit ba019977 authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

added new (now default) xyz plot

parent 491e3506

misc/nxs_xyz.py

+2 −2
Original line number Diff line number Diff line
@@ -7,7 +7,7 @@ import numpy as np 
import matplotlib.pyplot as plt



from pysen.inout.scans import XYZScan

from pysen.plot.xyzplotlib import xyz_decomposition, plot_xyz_nexus

from pysen.plot.xyzplotlib import plot_xyz_nexus



def plot_xyz(filename, **kwargs):

    scan = XYZScan()
@@ -90,7 +90,7 @@ def main(): 
    kwargs = vars(args)

    filenames = kwargs.pop('filename')

    for file_name in filenames:

        plot_xyz(file_name, **kwargs)

        plot_xyz_nexus(file_name, **kwargs)



    if args.show:

        plt.show()

pysen/plot/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -9,4 +9,4 @@ 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

                           plot_magnetic_fields, plot_map)           # NOQA

from .xyzplotlib  import plot_xyz                                    # NOQA
 
from .xyzplotlib  import plot_xyz, plot_xyz_nexus                    # NOQA

pysen/plot/nseplot.py

+36 −7
Original line number Diff line number Diff line
@@ -19,7 +19,7 @@ from pysen.config import INST_POSITIONS, INST_MODES, DEFAULT_ACCELERATOR_POWER, 
from pysen.inout  import convert_to_hdf

from pysen.echo   import get_symmetry_phase, make_phase_table

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

                           plot_xyz, plot_magnetic_fields,

                           plot_xyz, plot_xyz_nexus, plot_magnetic_fields,

                           plot_coverage,

                           plot_diffrun, plot_transmission, plot_datreat,

                           get_colormap)
@@ -48,8 +48,8 @@ action_atari = functools.partial(action_default, action=plot_atari) 
action_maps   = functools.partial(action_default, action=plot_map)

action_bfield = functools.partial(action_default, action=plot_magnetic_fields)



def action_xyz(filenames, **kwargs):

    "default action for xyz"

def action_old_xyz(filenames, **kwargs):

    "default action for old xyz plot"

    outdir    = kwargs.pop('outdir')

    overwrite = kwargs.pop('overwrite')

    savefig   = kwargs.pop('savefig')
@@ -66,6 +66,16 @@ def action_xyz(filenames, **kwargs): 
    if savefig:

        plt.savefig(savefig)



def action_xyz(filenames, **kwargs):

    "default action for xyz (new)"

    _outdir    = kwargs.pop('outdir')

    _overwrite = kwargs.pop('overwrite')

    savefig   = kwargs.pop('savefig')

    for filename in filenames:

        plot_xyz_nexus(filename, **kwargs)

        if savefig:

            plt.savefig(savefig)





def action_diffrun(filenames, **kwargs):

    "action for diffrun"
@@ -354,9 +364,9 @@ def add_atari_options(subparser, parents=None): 
    pars.add_argument('--phase0' , dest='phase0', type=float,

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



def add_xyz_options(subparser, parents=None):

def add_old_xyz_options(subparser, parents=None):

    "xyz options"

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

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

                      help='xyz plot (.dat or .h5 files)',

                      description='create xyz analysis plot')

    pars.set_defaults(overwrite=False, qmin=0, qmax=np.inf, deltaq=0.005, details=False)
@@ -370,6 +380,22 @@ def add_xyz_options(subparser, parents=None): 
    pars.add_argument('--details', dest='details', action='store_true',

                      help='print more details of xyz analysis')



def add_xyz_options(subparser, parents=None):

    "xyz options"

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

                      help='xyz plot .nxs.h5 file(s)',

                      description='create xyz analysis plot')

    pars.set_defaults(overwrite=False, qmin=0, qmax=np.inf, deltaq=0.005, details=False)

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

#    pars.add_argument('--qmin', dest='qmin', type=float,

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

#    pars.add_argument('--qmax', dest='qmax', type=float,

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

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

#                      help='q histogram bin witdth')

#    pars.add_argument('--details', dest='details', action='store_true',

#                      help='print more details of xyz analysis')



def add_diffrun_options(subparser, parents=None):

    "diffrun options"

    pars = subparser.add_parser('diffrun', parents=parents,
@@ -543,7 +569,7 @@ def main(): 
    add_echo_options(subparsers, parents=[pars_com, pars_tof, pars_pix])

    # atari plot

    add_atari_options(subparsers, parents=[pars_com, pars_tof, pars_pix, pars_zsc])

    # xyz plot

    # xyz plot (new)

    add_xyz_options  (subparsers, parents=[pars_com, pars_tof, pars_pix, pars_zsc])

    # diffrun plot

    add_diffrun_options(subparsers, parents=[pars_com, pars_tof])
@@ -559,6 +585,8 @@ def main(): 
    add_qtau_options(subparsers, parents=[pars_com,])

    # phase table

    add_ptab_options(subparsers, parents=[pars_com,pars_tof, pars_pix])

    # xyz2 plot (old)

    add_old_xyz_options  (subparsers, parents=[pars_com, pars_tof, pars_pix, pars_zsc])



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

    args = parser.parse_args()
@@ -578,7 +606,8 @@ def main(): 
                    transmission=action_transmission, tr=action_transmission,

                    datreat=action_datreat, dtr=action_datreat,

                    qtau=action_qtau, qt=action_qtau,

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

                    phase_table=action_phase_table, pt=action_phase_table,

                    old_xyz=action_old_xyz).get(args.command, None)

    if action is None:

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

pysen/plot/xyzplotlib.py

+36 −8
Original line number Diff line number Diff line
@@ -12,6 +12,7 @@ import matplotlib.pyplot as plt 
from   matplotlib import colors



from .. import config, get_q, ANGSTROM

from ..inout.scans import XYZScan

from .plotutil import norm_pix, get_pix
@@ -23,23 +24,18 @@ def xyz_decomposition(xyzdata, errors=False): 
    th six keys: {x,y,z}_{up,dn}"""



    res = {}



    # sum of x, y and z  measurements

    sX  = xyzdata['x_up'] + xyzdata['x_dn']

    sY  = xyzdata['y_up'] + xyzdata['y_dn']

    sZ  = xyzdata['z_up'] + xyzdata['z_dn']

    #







    # diff up-down for x, y and z measurements

    dX  = xyzdata['x_up'] - xyzdata['x_dn']

    dY  = xyzdata['y_up'] - xyzdata['y_dn']

    dZ  = xyzdata['z_up'] - xyzdata['z_dn']

    

    # sum of all up

    sUP     =    xyzdata['z_up'] + xyzdata['x_up'] + xyzdata['y_up']

    sDN     =    xyzdata['z_dn'] + xyzdata['x_dn'] + xyzdata['y_dn']



    # "magnetic" sum of up/down

    sM_UP  = +2*xyzdata['z_up'] - xyzdata['x_up'] - xyzdata['y_up']

    sM_DN  = -2*xyzdata['z_dn'] + xyzdata['x_dn'] + xyzdata['y_dn']
@@ -419,7 +415,7 @@ def plot_xyz_single_nexus(data, info, fig, axes, **kwargs): 
    data['selection_counts'] = cnts.sum()





def plot_xyz_nexus(data, info, **kwargs):

def plot_xyz_nexus_data(data, info, **kwargs):

    "plot xyz"

    #normalize = kwargs.pop('normalize', False)

    #savefile  = kwargs.pop('savefile' , None)
@@ -452,4 +448,36 @@ def plot_xyz_nexus(data, info, **kwargs): 
    #    self.xyz_analysis()

    #except KeyError as e:

    #    self.log.info("%s: key %s missing", self.info['base'], e)



def plot_xyz_nexus(filename, **kwargs):

    "plot NeXus NSE XYZ scan file"

    scan = XYZScan()

    scan.read_nexus(filename, **kwargs)



    plot_xyz_nexus_data(scan.data, scan.info, **kwargs)



    log = logging.getLogger()



    rates = {}

    base  = scan.info['base']

    for key, data in scan.data.items():

        rates[key]=0.0

        if data['pcharge']>0:

            counts = data['selection_counts']

            scale  = data['pcharge']/1e12

            rates[key]        = counts/scale

            rates[key+'_sig'] = np.sqrt(counts)/scale

            log.info("%s: %-6.6s = (%9.1f +/- %9.1f) counts/C", base, key.upper(), rates[key], rates[key+'_sig'])

        #

    res = xyz_decomposition(rates, errors=True)

    #

    stot = res['sum_ave']

    log.info("%s:", base)

    for key in ('n_coh', 'i_inc', 'm_mag'):

        log.info("%s: %-6.6s = (%9.1f +/- %9.1f) counts/C  (%5.2f +/- %4.2f)%%",

            base, key.upper(), res[key], res[key+'_sig'], res[key]/stot*100, res[key+'_sig']/stot*100)

    for key in ('m_up/2', 'm_dn/2',):

        log.info("%s: %-6.6s = (%9.1f +/- %9.1f) counts/C",

            base, key.upper(), res[key], res[key+'_sig'])

    log.info("%s: TOT    = %9.1f counts/C", base, stot)

#EOF