toward the grand unification (85d7a80e) · Commits · Zolnierczuk, Piotr / pysen

README.rst

+3 −1

Original line number	Diff line number	Diff line

		A bunch of Python scripts useful (hopefully) for neutron spin echo experiments.
		The pysen package is a collection of Python modules and scripts
		for the SNS-NSE instrument (BL-15)
		but may be also useful for any neutron spin echo experimenter.

pysen/plot/nseplot.py

+180 −62

Original line number	Diff line number	Diff line
		@@ -8,15 +8,97 @@ 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_magnetic_fields,
		plot_diffrun, plot_transmission )

		def action_default(filenames, **kwargs):
		action = kwargs.pop('action')
		tau = kwargs.pop('tau')
		outdir = kwargs.pop('outdir')
		savefig = kwargs.pop('savefig')
		log = kwargs.pop('log')
		to_show = False
		for filename in filenames:
		try:
		basename , ext = os.path.splitext(os.path.basename(filename))
		if ext != ".h5":
		log.info('converting %s to HDF', basename)
		filename = convert_to_hdf(filename, outdir, data_type='echo')
		#
		with h5py.File(filename, 'r') as hdf5file:
		action(hdf5file, tau, **kwargs)
		if savefig:
		plt.savefig(basename+'-'+savefig)
		else:
		to_show = True
		except FileNotFoundError as exc:
		print(exc)
		return to_show

		def action_diffrun(filenames, **kwargs):
		savefig = kwargs.pop('savefig')
		log = kwargs.pop('log')
		_, axis = plt.subplots(figsize=(8,8))
		plot_diffrun(axis, filenames, **kwargs)
		if savefig:
		plt.savefig(savefig)
		else:
		to_show = True
		return to_show

		def action_transmission(filenames, **kwargs):
		savefig = kwargs.pop('savefig')
		spectrum_only = kwargs.pop('spectrum_only')
		log = kwargs.pop('log')

		to_show = True
		ax1 = None
		if spectrum_only:
		_, ax0 = plt.subplots(1,1, figsize=(8,6))
		else:
		_, (ax0, ax1) = plt.subplots(2,1, figsize=(8,6), sharex=True)
		#_, (ax0, ax1) = plt.subplots(2,1, figsize=(args.figwidth, args.figheight), sharex=True)

		try:
		plot_transmission(ax0, ax1, filenames, **kwargs)
		except (OSError,RuntimeError) as e:
		print(e)

		if savefig:
		plt.savefig(savefig)
		else:
		to_show = True

		return to_show



		def arguments_selection(pars, pix=True, tof=True):
		"""
		"""
		if tof:
		pars.add_argument('--t1' , '-b', dest='tbin1', type=int,
		help='set min TOF bin (default=%(default)s)')
		pars.add_argument('--t2' , '-B', dest='tbin2', type=int,
		help='set max TOF bin (default=%(default)s)')
		if pix:
		pars.add_argument('--x1' , dest='xpix1', type=int,
		help='set min X pix (default=%(default)s)')
		pars.add_argument('--x2' , dest='xpix2', type=int,
		help='set max X pix (default=%(default)s)')
		pars.add_argument('--y1' , dest='ypix1', type=int,
		help='set min Y pix (default=%(default)s)')
		pars.add_argument('--y2' , dest='ypix2', type=int,
		help='set max Y pix (default=%(default)s)')
		pars.add_argument('--whole-detector', '-W', dest='whole_detector', action='store_true',
		help='show sum over entire detector area')

		def main():
		"the main"

		plot_action = dict(echo=plot_echo, atari=plot_atari, maps=plot_map, bfield=plot_magnetic_fields)
		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)
		@@ -35,8 +117,6 @@ def main():
		map_type='all', phase0=None,
		incoherent=False, max_chi2=1e3)
		parser.add_argument('file', metavar='filename', help='file to process', nargs='+')
		parser.add_argument('--tau', '-t', dest='tau', type=int,
		help='set tau to display (default=%(default)s)')
		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',
		@@ -53,8 +133,10 @@ def main():


		# echo plot
		parser_echo = subparsers.add_parser('echo', help='plot echo', parents=[parser])
		parser_echo = subparsers.add_parser('echo', help='plot echo (.echo or .h5 files)', parents=[parser])
		grp_echo = parser_echo.add_argument_group('echo plot options')
		grp_echo.add_argument('--tau', '-t', dest='tau', type=int,
		help='set tau to display (default=%(default)s)')
		grp_echo.add_argument('--center-only' , '-C', dest='center_only', action='store_true',
		help='show only center patch')
		grp_echo.add_argument('--only-echo', dest='only_echo', action='store_true',
		@@ -65,43 +147,47 @@ def main():
		help='use the same vertical scale for all pixels')
		grp_echo.add_argument('--num-pix', '-N', dest='npix', metavar='N', type=int,
		help='set pixel binning (default=%(default)s)')
		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')
		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
		parser_atari = subparsers.add_parser('atari', help='atari plot', parents=[parser])
		parser_atari = subparsers.add_parser('atari', help='atari plot (.echo or .h5 files)', parents=[parser])
		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)')
		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')
		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')
		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,
		@@ -113,26 +199,67 @@ def main():
		grp_atari.add_argument('--phase0' , dest='phase0', type=float,
		help='set inital phase for echo fitting (default=%(default)s)')

		# transmission plot


		# map plot
		parser_map = subparsers.add_parser('maps', help='plot maps', parents=[parser])
		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', parents=[parser])
		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)')

		# 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')
		grp_diffrun.set_defaults(selection=None, power=DEFAULT_ACCELERATOR_POWER)
		grp_diffrun.add_argument('--up', '-u', dest='selection', action='append_const', const='up',
		help="plot 'up' counts")
		grp_diffrun.add_argument('--down', '-d', dest='selection', action='append_const', const='down',
		help="plot 'down' counts")
		grp_diffrun.add_argument('--coherent', '-c', dest='selection', action='append_const', const='coherent',
		help="plot coherent deconvoluted")
		grp_diffrun.add_argument('--incoherent', '-i', dest='selection', action='append_const', const='incoherent',
		help="plot incoherent deconvoluted")
		grp_diffrun.add_argument('--ratio', '-r', dest='selection', action='append_const', const='flip_ratio',
		help="plot flip ratio (up/down)")
		grp_diffrun.add_argument('--average', '-a', dest='selection', action='append_const', const='average',
		help="plot (up+down)/2 sum")
		grp_diffrun.add_argument('--coherent-ratio', '-C', dest='selection', action='append_const', const='coherent_ratio',
		help="plot coherent/incoherent ratio")
		#
		arguments_selection(grp_diffrun, pix=False)
		grp_diffrun.add_argument('--logscale', '-l', dest='log_scale', action='store_true',
		help="plot in semilogy")
		grp_diffrun.add_argument('--att', '-A', dest='att_table', action='store_true',
		help="use attenuation table")

		# transmission plot
		parser_trans = subparsers.add_parser('transmission', help='plot transmission data', parents=[parser])
		grp_trans= parser_trans.add_argument_group('transmission plot options')
		grp_trans.set_defaults(log_scale=False, spectrum_only=False, pos='p2')
		grp_trans.add_argument('--pos' , '-p', dest='pos' ,
		help='set instrument position: p1, p2, p3 or p4 (default %(default)s)')
		arguments_selection(grp_trans, pix=False)
		grp_trans.add_argument('--logscale', '-l', dest='logscale', action='store_true',
		help="plot in semilogy")
		grp_trans.add_argument('--spectrum-only', '-w', dest='spectrum_only', action='store_true',
		help="plot only wavelength spectrum")
		grp_trans.add_argument('--poly', '-P', type=int, dest='polyfit', metavar='deg',
		help='set polynomial degree to fit (default=%(default)s)')
		grp_trans.add_argument('--echodet', '-e', dest='echodet', action='store_true',
		help='report transmission for echodet 1/T')

		# ===================================
		args = parser_top.parse_args()
		log = setup_logger(args.loglevel)
		log.debug('program arguments %s', args)
		@@ -141,24 +268,15 @@ def main():
		if args.savefig:
		plt.switch_backend('Agg')


		kwargs = vars(args)
		to_show = False
		for filename in args.file:
		try:
		basename , ext = os.path.splitext(os.path.basename(filename))
		if ext != ".h5":
		log.info('converting %s to HDF', basename)
		filename = convert_to_hdf(filename, args.outdir, data_type='echo')
		#
		with h5py.File(filename, 'r') as hdf5file:
		plot_action[args.what](hdf5file, iecho=args.tau, **kwargs)
		if args.savefig:
		plt.savefig(basename+'-'+args.savefig)
		else:
		to_show = True
		except FileNotFoundError as exc:
		print(exc)

		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)
		if args.what in ('diffrun', ):
		to_show = action_diffrun(args.file, log=log, **kwargs)
		if args.what in ('transmission', ):
		to_show = action_transmission(args.file, log=log, **kwargs)
		if to_show:
		plt.show()

pysen/plot/qplot.py

+12 −12

Original line number	Diff line number	Diff line
		@@ -262,9 +262,9 @@ def _get_q(q, wavelength, t1=0, t2=-1):
		def plot_diffrun(axis, filenames, **kwargs):
		"process files"

		what = kwargs.pop('what', None) or ('up', 'down')
		t1 = kwargs.pop('tmin', None)
		t2 = kwargs.pop('tmax', None)
		selection = kwargs.pop('selection', None) or ('up', 'down')
		t1 = kwargs.pop('tbin1', None)
		t2 = kwargs.pop('tbin2', None)
		logscale = kwargs.pop('log_scale', False)
		output = kwargs.pop('output', None)
		power = kwargs.pop('power', 1.4)
		@@ -349,30 +349,30 @@ def plot_diffrun(axis, filenames, **kwargs):
		if out:
		np.savetxt(out, data.T, fmt='%.3g', header = "%s\nQ counts err" % label)

		if 'up' in what:
		if 'up' in selection:
		_make_plot(axis, (q0, cup, ecup ), marker='^', lbl='up')
		axis0 = axis
		if 'down' in what:
		if 'down' in selection:
		_make_plot(axis, (q1, cdn, ecdn ), marker='v', lbl='down')
		axis0 = axis
		if 'coherent' in what:
		if 'coherent' in selection:
		_make_plot(axis, (qmean, coherent, ecoherent ), marker='^', lbl='C')
		axis0 = axis
		if 'incoherent' in what:
		if 'incoherent' in selection:
		_make_plot(axis, (qmean, incoherent, eincoherent ), marker='v', lbl='I')
		axis0 = axis
		if 'average' in what:
		if 'average' in selection:
		average = (coherent+incoherent)/2
		eaverage = sqrt(ecoherent2+eincoherent2)
		_make_plot(axis, (qmean, average, eaverage), marker='s', lbl='<A>')
		axis0 = axis

		# ratios
		if 'flip_ratio' in what:
		if 'flip_ratio' in selection:
		#fratio = np.where(fratio>1.0, fratio, 1.0/fratio)
		if axis1 is None: axis1 = axis.twinx()
		_make_plot(axis1, (qmean, fratio, eratio ), marker='o', lbl='FR')
		if 'coherent_ratio' in what:
		if 'coherent_ratio' in selection:
		cratio = (2*fratio - 1)/3
		ecratio = (2*eratio)/3
		if axis1 is None: axis1 = axis.twinx()
		@@ -404,8 +404,8 @@ def plot_transmission(ax0, ax1, filenames, **kwargs):
		polyfit = kwargs.get('polyfit', None)
		echodet = kwargs.get('echodet', False)
		pos = kwargs.get('pos', 'p2')
		tmin = kwargs.get('tmin', 0)
		tmax = kwargs.get('tmax', None)
		tmin = kwargs.get('tbin1', 0)
		tmax = kwargs.get('tbin2', None)

		tcounts = collections.OrderedDict()

scripts/plot_diffrun.py

+10 −10

Original line number	Diff line number	Diff line
		@@ -14,31 +14,31 @@ from pysen.plot import plot_diffrun
		def main():
		"main entry"
		parser = argparse.ArgumentParser()
		parser.set_defaults(what=None,
		parser.set_defaults(selection=None,
		log_scale=False, tmin=None, tmax=-1, att_table=None,
		power=DEFAULT_ACCELERATOR_POWER,
		plotfile=None, output=None)
		parser.add_argument('file', metavar='filename',
		help='file to process', nargs='+')
		parser.add_argument('--up', '-u', dest='what', action='append_const', const='up',
		parser.add_argument('--up', '-u', dest='selection', action='append_const', const='up',
		help="plot 'up' counts")
		parser.add_argument('--down', '-d', dest='what', action='append_const', const='down',
		parser.add_argument('--down', '-d', dest='selection', action='append_const', const='down',
		help="plot 'down' counts")
		parser.add_argument('--coherent', '-c', dest='what', action='append_const', const='coherent',
		parser.add_argument('--coherent', '-c', dest='selection', action='append_const', const='coherent',
		help="plot coherent and incoherent deconvoluted")
		parser.add_argument('--incoherent', '-i', dest='what', action='append_const', const='incoherent',
		parser.add_argument('--incoherent', '-i', dest='selection', action='append_const', const='incoherent',
		help="plot coherent and incoherent deconvoluted")
		#
		parser.add_argument('--ratio', '-r', dest='what', action='append_const', const='flip_ratio',
		parser.add_argument('--ratio', '-r', dest='selection', action='append_const', const='flip_ratio',
		help="plot flip ratio")
		parser.add_argument('--average', '-a', dest='what', action='append_const', const='average',
		parser.add_argument('--average', '-a', dest='selection', action='append_const', const='average',
		help="plot (up+down)/2 sum")
		parser.add_argument('--coherent-ratio', '-C', dest='what', action='append_const', const='coherent_ratio',
		parser.add_argument('--coherent-ratio', '-C', dest='selection', action='append_const', const='coherent_ratio',
		help="plot coherent/incoherent ratio")
		#
		parser.add_argument('--tmin', '-t', dest='tmin', type=int,
		parser.add_argument('--tmin', '-t', metavar='tmin', dest='tbin1', type=int,
		help='')
		parser.add_argument('--tmax', '-T', dest='tmax', type=int,
		parser.add_argument('--tmax', '-T', metavar='tmax', dest='tbin2', type=int,
		help='')
		parser.add_argument('--logscale', '-l', dest='log_scale', action='store_true',
		help="plot in semilogy")

scripts/plot_transmission.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -24,9 +24,9 @@ def main():
		help="plot in semilogy")
		parser.add_argument('--spectrum-only', '-w', dest='spectrum_only', action='store_true',
		help="plot only wavelength spectrum")
		parser.add_argument('--tmin', '-t', type=int, dest='tmin',
		parser.add_argument('--tmin', '-t', type=int, dest='tbin1', metavar='tmin',
		help='set min TOF channel (default=%(default)s)')
		parser.add_argument('--tmax', '-T', type=int, dest='tmax',
		parser.add_argument('--tmax', '-T', type=int, dest='tbin2', metavar='tmax',
		help='set max TOF channel (default=%(default)s)')
		parser.add_argument('--poly', '-P', type=int, dest='polyfit', metavar='deg',
		help='set polynomial degree to fit (default=%(default)s)')