fixing plot_diffrun (320f0f3a) · Commits · Zolnierczuk, Piotr / pysen

pysen/plot/qplot.py

+103 −45

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@ import numpy as np
		from matplotlib import cm
		from matplotlib.patches import Polygon
		from matplotlib.colors import LogNorm
		from numpy import sqrt
		#pylint: disable=no-name-in-module
		from scipy.spatial import ConvexHull

		@@ -129,7 +130,7 @@ def _plot_counts(ax, x, cnts, label, fmt='ko-', normalize=None):
		"plot counts as a function of phase point"
		if x is None:
		x = range(1,len(cnts)+1)
		ecnts = np.sqrt(cnts*1.0)
		ecnts = sqrt(cnts*1.0)
		if normalize is not None:
		cnts = cnts *1.0/normalize
		ecnts = ecnts*1.0/normalize
		@@ -254,7 +255,7 @@ def _get_q(q, wavelength, t1=0, t2=-1):
		lave = np.average(wavelength[:,t1:t2])
		dlam = np.abs(wavelength[:,t1]-wavelength[:,t2])/2.0
		q = q*wavelength[:,-1]/lave
		dq = np.sqrt((dlam/lave)*2) #+ (0.5dtheta/np.tan(theta/2.0))**2)
		dq = sqrt((dlam/lave)*2) #+ (0.5dtheta/np.tan(theta/2.0))**2)
		return q, dq


		@@ -327,7 +328,7 @@ def plot_diffrun_old(axis, filenames, **kwargs):
		else:
		q, dq = _get_q(q, wlen, t1, t2)

		data = np.vstack( (q, dq, cntfac, np.sqrt(cnt1.0)*fac) )
		data = np.vstack( (q, dq, cntfac, sqrt(cnt1.0)*fac) )
		data = data[:, data[0].argsort()]
		sym = {'up':'^', 'down':'v'}.get(lbl,'*')
		#
		@@ -355,7 +356,6 @@ def plot_diffrun_old(axis, filenames, **kwargs):
		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)
		@@ -364,24 +364,24 @@ def plot_diffrun_old(axis, filenames, **kwargs):
		fac = (att0[:ndat]pc1[:ndat])/(att1[:ndat]pc0[:ndat])
		fratio = cnt0[:ndat]/cnt1[:ndat]
		eratio = 1.0/cnt0[:ndat] + 1.0/cnt1[:ndat]
		eratio = np.sqrt(eratio)fratiofac
		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 = np.sqrt(cnt0[:ndat])*fup
		exdn = np.sqrt(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 = np.sqrt(exup*2 + 1/4exdn**2)
		ecoherent = sqrt(exup*2 + 1/4exdn**2)
		eincoherent = 3/2*exdn


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

		if what=='flip_ratio':
		fratio = np.where(fratio>1.0, fratio, 1.0/fratio)
		@@ -408,7 +408,7 @@ def plot_diffrun_old(axis, filenames, **kwargs):

		if what=='average':
		average = (coherent+incoherent)/2
		eaverage = np.sqrt(ecoherent2+eincoherent2)
		eaverage = sqrt(ecoherent2+eincoherent2)
		data = np.vstack( (qmean, average, eaverage) )
		data = data[:, data[0].argsort()]
		axis.errorbar(data[0], data[1], yerr=data[2],
		@@ -449,11 +449,10 @@ def plot_diffrun_old(axis, filenames, **kwargs):
		axis.legend(loc='best')
		axis.grid(True)


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

		what = kwargs.pop('what', ('up', 'down'))
		what = kwargs.pop('what', None) or ('up', 'down')
		t1 = kwargs.pop('tmin', None)
		t2 = kwargs.pop('tmax', None)
		logscale = kwargs.pop('log_scale', False)
		@@ -473,48 +472,107 @@ def plot_diffrun_new(axis, filenames, **kwargs):

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

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

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

		updn = {}

		log.info(filename)
		result = meta
		acolor = cmap((_i)/nfiles)
		ndat = len(result)//2

		for off, lbl in zip((0, 1), ('up', 'down')):
		q = meta[off::2, 0] # q_min
		pc = meta[off::2, 1] # proton charge
		q = result[:, 0] #
		if noqerr:
		cnt = meta[off::2, 2] # detector sum
		q0, dq0 = q[0::2], None
		q1, dq1 = q[1::2], None
		cnt = result[::, 2] # detector sum
		else:
		cnt = np.sum(det[off::2,0,t1:t2], axis=-1)
		#win = result[off::2, 3] # detector win
		att = meta[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
		q0, dq0 = _get_q(q[0::2], wlen, t1, t2)
		q1, dq1 = _get_q(q[1::2], wlen, t1, t2)
		cnt = np.sum(det[:,0,t1:t2], axis=-1)

		if noqerr:
		dq = np.zeros_like(q)
		else:
		q, dq = _get_q(q, wlen, t1, t2)
		# 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]
		#
		fup = att0/pc0*PCHARGE_PER_SECOND
		fdn = att1/pc1*PCHARGE_PER_SECOND
		cup = cnt0*fup
		cdn = cnt1*fdn
		ecup = sqrt(cnt0)*fup
		ecdn = sqrt(cnt1)*fdn

		# flip ratio
		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
		# up = c + 1/3i
		# dn = 2/3i
		coherent = cup[:ndat] - 1/2*cdn[:ndat]
		incoherent = 3/2*cdn[:ndat]
		ecoherent = sqrt(ecup[:ndat]*2 + 1/4ecdn[:ndat]**2)
		eincoherent = 3/2*ecdn[:ndat]

		qmean = 0.5*(q0[:ndat]+q1[:ndat])

		data = np.vstack( (q, dq, cntfac, np.sqrt(cnt1.0)*fac) )
		updn[off] = data[:, data[0].argsort()]
		#if out:
		# np.savetxt(out, data.T, fmt='%.3g', footer=' ',
		# header = "%s '%s'\nQ counts err" % (filename, lbl))
		def _make_plot(axis, data, **kwargs):
		kwargs.setdefault('ls', '--')
		kwargs.setdefault('lw', 1)
		kwargs.setdefault('color', acolor)
		data = np.vstack( data )
		data = data[:, data[0].argsort()]
		label="%s (%s)" % (os.path.basename(filename), kwargs.pop('lbl'))
		axis.errorbar(data[0], data[1], yerr=data[2], label=label, **kwargs)
		if out:
		np.savetxt(out, data.T, fmt='%.3g', header = "%s\nQ counts err" % label)

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

		# ratios
		if 'flip_ratio' in what:
		#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:
		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')

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

		plot_diffrun = plot_diffrun_new
		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
		@@ -2,8 +2,8 @@
		PySEN revision module
		"""
		import sys
		__version__ = "0.71"
		__release__ = "dev2"
		__version__ = "0.72"
		__release__ = "dev1"
		__date__ = "Aug 2, 2022"

		def version(full=False):

scripts/plot_diffrun.py

+5 −2

Original line number	Diff line number	Diff line
		@@ -80,10 +80,13 @@ def main():
		help="plot 'up' counts")
		parser.add_argument('--down', '-d', dest='what', action='append_const', const='down',
		help="plot 'down' counts")
		parser.add_argument('--ratio', '-r', dest='what', action='append_const', const='flip_ratio',
		help="plot flip ratio")
		parser.add_argument('--coherent', '-c', dest='what', action='append_const', const='coherent',
		help="plot coherent and incoherent deconvoluted")
		parser.add_argument('--incoherent', '-i', dest='what', action='append_const', const='incoherent',
		help="plot coherent and incoherent deconvoluted")
		#
		parser.add_argument('--ratio', '-r', dest='what', action='append_const', const='flip_ratio',
		help="plot flip ratio")
		parser.add_argument('--average', '-a', dest='what', 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',