diffrun cleanup (1c751479) · Commits · Zolnierczuk, Piotr / pysen

pysen/plot/qplot.py

+18 −197

Original line number	Diff line number	Diff line
		@@ -259,196 +259,6 @@ def _get_q(q, wavelength, t1=0, t2=-1):
		return q, dq


		def plot_diffrun_old(axis, filenames, **kwargs):
		"process files"

		what = kwargs.pop('what', None)
		up = kwargs.pop('up', True)
		down = kwargs.pop('down', True)
		t1 = kwargs.pop('tmin', None)
		t2 = kwargs.pop('tmax', None)
		logscale = kwargs.pop('log_scale', False)
		output = kwargs.pop('output', None)
		power = kwargs.pop('power', 1.4)
		use_att = kwargs.pop('att_table', False)

		log = logging.getLogger()

		selection = []
		title = 'Diffraction Run Plot'
		out = None
		lw = 1
		cmap = cm.get_cmap('hsv')

		if output:
		out = open(output, 'wb') #pylint: disable=consider-using-with

		if what:
		up=down=False
		ylabel = { 'flip_ratio' : 'Flip Ratio',
		'coherent_ratio' : 'Coherent/Incoherent Ratio',
		}.get(what, 'Rates [arb.]')
		else:
		ylabel = 'Count Rate [counts/s] at %.1f MW' % power
		if up:
		selection.append((0,'up'))
		if down:
		selection.append((1,'down'))

		noqerr = t1 is None or t2 is None
		nfiles = len(filenames)

		for _i, filename in enumerate(filenames):
		res = read_diffrun(filename) #
		result = res.get('summary')
		wlen = res.get('wavelength')
		det = res.get('detector')
		#mon1 = res.get('monitor1')
		#mon2 = res.get('monitor2')

		acolor = cmap((_i)/nfiles)
		wlen = wlen/ANGSTROM

		log.info(filename)

		for off, lbl in selection: # zip((0, 1), ('up', 'down')):
		q = result[off::2, 0] # q_min
		pc = result[off::2, 1] # proton charge
		if noqerr:
		cnt = result[off::2, 2] # detector sum
		else:
		cnt = np.sum(det[off::2,0,t1:t2], axis=-1)
		#win = result[off::2, 3] # detector win
		att = result[off::2, 4]*1.0 if use_att else np.ones_like(pc) # attenuator table
		#lmax = result[off::2, 5]/ANGSTROM
		fac = (att/pc)*PCHARGE_PER_SECOND

		if noqerr:
		dq = np.zeros_like(q)
		else:
		q, dq = _get_q(q, wlen, t1, t2)

		data = np.vstack( (q, dq, cntfac, sqrt(cnt1.0)*fac) )
		data = data[:, data[0].argsort()]
		sym = {'up':'^', 'down':'v'}.get(lbl,'*')
		#
		axis.errorbar(data[0], data[2], yerr=data[3], #xerr=data[1],
		marker=sym, ls='--',
		color=acolor, lw=lw, label="%s (%s)" % (os.path.basename(filename), lbl))
		if out:
		np.savetxt(out, data.T, fmt='%.3g', footer=' ',
		header = "%s '%s'\nQ counts err" % (filename, lbl))

		if what is not None:
		ndat = len(result)//2

		q = result[:, 0] #
		if noqerr:
		q0 = q[0::2]
		q1 = q[1::2]
		cnt = result[::, 2] # detector sum
		else:
		q0, _ = _get_q(q[0::2], wlen, t1, t2)
		q1, _ = _get_q(q[1::2], wlen, t1, t2)
		cnt = np.sum(det[:,0,t1:t2], axis=-1)

		#up count
		pc0 = result[0::2, 1]
		att0 = result[0::2, 4]*1.0 if use_att else np.ones_like(pc0)
		cnt0 = cnt[0::2]
		#down count
		pc1 = result[1::2, 1]
		att1 = result[1::2, 4]*1.0 if use_att else np.ones_like(pc1)
		cnt1 = cnt[1::2]

		fac = (att0[:ndat]pc1[:ndat])/(att1[:ndat]pc0[:ndat])
		fratio = cnt0[:ndat]/cnt1[:ndat]
		eratio = 1.0/cnt0[:ndat] + 1.0/cnt1[:ndat]
		eratio = sqrt(eratio)fratiofac
		#
		fup = att0[:ndat]/pc0[:ndat]*PCHARGE_PER_SECOND
		fdn = att1[:ndat]/pc1[:ndat]*PCHARGE_PER_SECOND
		xup = cnt0[:ndat]*fup
		xdn = cnt1[:ndat]*fdn
		exup = sqrt(cnt0[:ndat])*fup
		exdn = sqrt(cnt1[:ndat])*fdn
		# up = c + 1/3i
		# dn = 2/3i
		coherent = xup - 1/2*xdn
		incoherent = 3/2*xdn
		ecoherent = sqrt(exup*2 + 1/4exdn**2)
		eincoherent = 3/2*exdn


		qmean = 0.5*(q0[:ndat]+q1[:ndat])
		#dqmean = sqrt(dq0[:ndat]2+dq1[:ndat]2)

		if what=='flip_ratio':
		fratio = np.where(fratio>1.0, fratio, 1.0/fratio)
		data = np.vstack( (qmean, fratio, eratio) )
		data = data[:, data[0].argsort()]
		axis.errorbar(data[0], data[1], yerr=data[2],
		fmt='o--', lw=lw, color=acolor,
		label="%s (%s)" % (os.path.basename(filename), 'FR'))
		if out:
		np.savetxt(out, data.T, fmt='%.3g', footer=' ',
		header="%s '%s'\nQ dQ FR err" % (filename, 'flip ratio'))

		if what=='coherent_ratio':
		fratio = (2*fratio - 1)/3
		eratio = (2*eratio)/3
		data = np.vstack( (qmean, fratio, eratio) )
		data = data[:, data[0].argsort()]
		axis.errorbar(data[0], data[1], yerr=data[2],
		fmt='s--', lw=lw, color=acolor,
		label="%s (%s)" % (os.path.basename(filename), 'C/I'))
		if out:
		np.savetxt(out, data.T, fmt='%.3g', footer=' ',
		header="%s '%s'\nQ dQ C/I err" % (filename, 'coherent/incoherent'))

		if what=='average':
		average = (coherent+incoherent)/2
		eaverage = sqrt(ecoherent2+eincoherent2)
		data = np.vstack( (qmean, average, eaverage) )
		data = data[:, data[0].argsort()]
		axis.errorbar(data[0], data[1], yerr=data[2],
		fmt='s--', lw=lw, color=acolor,
		label="%s (%s)" % (os.path.basename(filename), '<A>'))
		if out:
		np.savetxt(out, data.T, fmt='%.3g', footer=' ',
		header="%s '%s'\nQ dQ A err" % (filename, 'average'))

		if what in ('coherent','incoherent','both'):
		if what in ('coherent','both'):
		data = np.vstack( (qmean, coherent, ecoherent) )
		data = data[:, data[0].argsort()]
		axis.errorbar(data[0], data[1], yerr=data[2],
		fmt='^--', lw=lw, color=acolor,
		label="%s (%s)" % (os.path.basename(filename), 'C'))
		if out:
		np.savetxt(out, data.T, fmt='%.3g', footer=' ',
		header="%s '%s'\nQ dQ C err" % (filename, 'coherent'))
		if what in ('incoherent','both'):
		data = np.vstack( (qmean, incoherent, eincoherent) )
		data = data[:, data[0].argsort()]
		axis.errorbar(data[0], data[1], yerr=data[2],
		fmt='v:', lw=lw, color=acolor,
		label="%s (%s)" % (os.path.basename(filename), 'I'))
		if out:
		np.savetxt(out, data.T, fmt='%.3g', footer=' ',
		header="%s '%s'\nQ dQ I err" % (filename, 'incoherent'))

		axis.set_yscale('log' if logscale else 'linear')

		if noqerr:
		axis.set_xlabel(r'$Q_{min}$ $\AA^{-1}$')
		else:
		axis.set_xlabel(r'$<Q>$ $\AA^{-1}$')
		axis.set_ylabel(ylabel)
		axis.set_title(title)
		axis.legend(loc='best')
		axis.grid(True)

		def plot_diffrun(axis, filenames, **kwargs):
		"process files"

		@@ -472,7 +282,7 @@ def plot_diffrun(axis, filenames, **kwargs):

		noqerr = t1 is None or t2 is None
		nfiles = len(filenames)
		ylabel = 'Count Rate [counts/s] at %.1f MW' % power
		axis0 = None
		axis1 = None

		for _i, filename in enumerate(filenames):
		@@ -541,16 +351,21 @@ def plot_diffrun(axis, filenames, **kwargs):

		if 'up' in what:
		_make_plot(axis, (q0, cup, ecup ), marker='^', lbl='up')
		axis0 = axis
		if 'down' in what:
		_make_plot(axis, (q1, cdn, ecdn ), marker='v', lbl='down')
		axis0 = axis
		if 'coherent' in what:
		_make_plot(axis, (qmean, coherent, ecoherent ), marker='^', lbl='C')
		axis0 = axis
		if 'incoherent' in what:
		_make_plot(axis, (qmean, incoherent, eincoherent ), marker='v', lbl='I')
		axis0 = axis
		if 'average' in what:
		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:
		@@ -561,18 +376,24 @@ def plot_diffrun(axis, filenames, **kwargs):
		cratio = (2*fratio - 1)/3
		ecratio = (2*eratio)/3
		if axis1 is None: axis1 = axis.twinx()
		_make_plot(axis1, (qmean, cratio, ecratio), marker='s', lbl='C/I')
		_make_plot(axis, (qmean, cratio, ecratio), marker='s', lbl='C/I')

		if axis0 is not None:
		axis0.set_yscale('log' if logscale else 'linear')
		axis0.legend(loc='best')
		axis0.grid(True, which='both')
		axis0.set_ylabel('Count Rate [counts/s] at %.1f MW' % power)
		if axis1 is not None:
		axis1.set_yscale('log' if logscale else 'linear')
		axis1.legend(loc='best')
		axis1.grid(True, which='both')
		axis1.set_ylabel('Ratio')

		axis.set_yscale('log' if logscale else 'linear')
		if noqerr:
		axis.set_xlabel(r'$Q_{min}$ $\AA^{-1}$')
		else:
		axis.set_xlabel(r'$<Q>$ $\AA^{-1}$')

		axis.set_ylabel(ylabel)
		axis.set_title(title)
		axis.legend(loc='best')
		axis.grid(True)


		def plot_transmission(ax0, ax1, filenames, **kwargs):

pysen/revision.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -3,8 +3,8 @@ PySEN revision module
		"""
		import sys
		__version__ = "0.72"
		__release__ = "dev1"
		__date__ = "Aug 2, 2022"
		__release__ = "dev2"
		__date__ = "Aug 3, 2022"

		def version(full=False):
		"get pysen version number"

scripts/plot_diffrun.py

+0 −57

Original line number	Diff line number	Diff line
		@@ -11,62 +11,6 @@ from pysen import version, setup_logger
		from pysen.config import DEFAULT_ACCELERATOR_POWER
		from pysen.plot import plot_diffrun


		def main_old():
		"main entry"
		parser = argparse.ArgumentParser()
		parser.set_defaults(up=True, down=True, what=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='+')
		group = parser.add_mutually_exclusive_group()
		group.add_argument('--up', '-u', dest='down', action='store_false',
		help="plot 'up' counts only")
		group.add_argument('--down', '-d', dest='up', action='store_false',
		help="plot 'down' counts only")

		group.add_argument('--ratio', '-r', dest='what', action='store_const', const='flip_ratio',
		help="plot flip ratio")
		group.add_argument('--coherent', '-c', dest='what', action='store_const', const='coherent',
		help="plot coherent and incoherent deconvoluted")
		group.add_argument('--average', '-a', dest='what', action='store_const', const='average',
		help="plot (coherent+incoherent)/2 sum")
		group.add_argument('--coherent-ratio', '-C', dest='what', action='store_const', const='coherent_ratio',
		help="plot coherent/incoherent ratio")

		parser.add_argument('--tmin', '-t', dest='tmin', type=int,
		help='')
		parser.add_argument('--tmax', '-T', dest='tmax', type=int,
		help='')
		parser.add_argument('--logscale', '-l', dest='log_scale', action='store_true',
		help="plot in semilogy")
		parser.add_argument('--att', '-A', dest='att_table', action='store_true',
		help="use attenuation table")

		parser.add_argument('--save', '-s', dest='plotfile')
		parser.add_argument('--out', '-o', dest='output')
		parser.add_argument('--version', action='version',
		version='%(prog)s pysen={version}'.format(version=version()))


		setup_logger()
		args = parser.parse_args()
		kwargs = vars(args)

		_, axis = plt.subplots(figsize=(8,8))
		try:
		plot_diffrun(axis, args.file, **kwargs)

		if args.plotfile:
		plt.savefig(args.plotfile)
		else:
		plt.show()
		except (OSError, RuntimeError) as e:
		print(e)


		def main():
		"main entry"
		parser = argparse.ArgumentParser()
		@@ -111,7 +55,6 @@ def main():
		setup_logger()
		args = parser.parse_args()
		kwargs = vars(args)
		print(kwargs)

		_, axis = plt.subplots(figsize=(8,8))
		try: