Commit 858849250845754b7085965916af5d20a05bf447 - xrayutilities

+9

-0

CHANGES.txt less more

	0	v1.0.3, 2013-10-25
	1
	2	* build_doc target for setup.py to help build docs (thanks to F. Picca)
	3	* fix python setup.py --help
	4	* add PseudoVoigt function in 1D
	5	* add Lorentzian peak shape in addition to Gaussian in new function
	6	multPeakFit
	7	* some minor bug fixes
	8
0	9	v1.0.2, 2013-09-17
1	10
2	11	* add documentation source to tarball

+12

-9

PKG-INFO less more

0	0	Metadata-Version: 1.1
1	1	Name: xrayutilities
2		Version: 1.0.2
	2	Version: 1.0.3
3	3	Summary: package for x-ray diffraction data evaluation
4	4	Home-page: http://xrayutilities.sourceforge.net
5	5	Author: Dominik Kriegner

163	163
164	164	in any web-browser, after the installation is finished.
165	165
166		To build the PDF documentation from the sources use sphinx:
167
168		sphinx-build -b latex doc/source doc/latex
169		cd doc/latex; make
	166	To build the PDF documentation from the docu-sources use:
	167
	168	python setup.py build_doc -b latex
	169	cd build/sphinx/latex; make
170	170
171		or generate a texinfo file using
172
173		sphinx-build -b texinfo doc/source doc/texinfo
174		cd doc/texinfo; make
	171	You will need sphinx and pdflatex including latex-recommended, latex-extra
	172	and fonts-recommended.
	173
	174	Or generate a texinfo file using
	175
	176	python setup.py build_doc -b texinfo
	177	cd build/sphinx/texinfo; make
175	178
176	179
177	180	PACKAGING

+9

-6

README.txt less more

155	155
156	156	in any web-browser, after the installation is finished.
157	157
158		To build the PDF documentation from the sources use sphinx:
	158	To build the PDF documentation from the docu-sources use:
159	159
160		sphinx-build -b latex doc/source doc/latex
161		cd doc/latex; make
	160	python setup.py build_doc -b latex
	161	cd build/sphinx/latex; make
162	162
163		or generate a texinfo file using
	163	You will need sphinx and pdflatex including latex-recommended, latex-extra
	164	and fonts-recommended.
164	165
165		sphinx-build -b texinfo doc/source doc/texinfo
166		cd doc/texinfo; make
	166	Or generate a texinfo file using
	167
	168	python setup.py build_doc -b texinfo
	169	cd build/sphinx/texinfo; make
167	170
168	171
169	172	PACKAGING

+1

-1

doc/source/conf.py less more

49	49	# The short X.Y version.
50	50	version = '1.0'
51	51	# The full version, including alpha/beta/rc tags.
52		release = '1.0.2'
	52	release = '1.0.3'
53	53
54	54	# The language for content autogenerated by Sphinx. Refer to documentation
55	55	# for a list of supported languages.

+18

-0

doc/source/examples.rst less more

380	380	:linenos:
381	381	:language: python
382	382
	383	A possible output of this script could be
	384
	385	.. code-block:: python
	386
	387	fitted parameters: epsilon: 8.0712e-08 (2,['Parameter convergence'])
	388	param: (cch1,cch2,pwidth1,pwidth2,tiltazimuth,tilt,detrot,outerangle_offset)
	389	param: 140.07 998.34 4.4545e-05 4.4996e-05 72.0 1.97 -0.792 -1.543
	390	please check the resulting data (consider setting plot=True)
	391	detector rotation axis / primary beam direction (given by user): ['z+', 'y-'] / x+
	392	detector pixel directions / distance: z- y+ / 1
	393	detector initialization with: init_area('z-','y+',cch1=140.07,cch2=998.34,Nch1=516,Nch2=516, pwidth1=4.4545e-05,pwidth2=4.4996e-05,distance=1.,detrot=-0.792,tiltazimuth=72.0,tilt=1.543)
	394	AND ALWAYS USE an (additional) OFFSET of -1.9741deg in the OUTER DETECTOR ANGLE!
	395
	396
	397	The output gives the fitted detector parameters and compiles the python code line one needs to use to initialize the detector.
	398	Important to note is that the outer angle offset which was determined by the fit (-1.9741 degree in the aboves example) is not included in the initialization of the detector parameters BUT needs to be used in every call to the q-conversion function as offset.
	399	This step needs to be performed manually by the user!
	400
383	401	Area detector (Variant 2)
384	402	^^^^^^^^^^^^^^^^^^^^^^^^^
385	403

~~doc/xrayutilities.info~~ less more

Binary diff not shown

+3

-3

examples/xrayutilities_experiment_kappa.py less more

31	31
32	32	print("angles: 0,0,0,90")
33	33	(qx,qy,qz) = qconv(0,0,0,90)
34		print("Q= %6.3f %6.3f %6.3f (Abs: %6.3f)" %(qx[0],qy[0],qz[0],numpy.linalg.norm((qx,qy,qz))))
	34	print("Q= %6.3f %6.3f %6.3f (Abs: %6.3f)" %(qx,qy,qz,numpy.linalg.norm((qx,qy,qz))))
35	35
36	36	print("angles: 90,0,0,90")
37	37	(qx,qy,qz) = qconv(90,0,0,90)
38		print("Q= %6.3f %6.3f %6.3f (Abs: %6.3f)" %(qx[0],qy[0],qz[0],numpy.linalg.norm((qx,qy,qz))))
	38	print("Q= %6.3f %6.3f %6.3f (Abs: %6.3f)" %(qx,qy,qz,numpy.linalg.norm((qx,qy,qz))))
39	39
40	40	print("angles: 0,90,0,90")
41	41	(qx,qy,qz) = qconv(0,90,0,90)
42		print("Q= %6.3f %6.3f %6.3f (Abs: %6.3f)" %(qx[0],qy[0],qz[0],numpy.linalg.norm((qx,qy,qz))))
	42	print("Q= %6.3f %6.3f %6.3f (Abs: %6.3f)" %(qx,qy,qz,numpy.linalg.norm((qx,qy,qz))))
43	43

+40

-3

setup.py less more

20	20	from distutils.fancy_getopt import FancyGetopt
21	21	import os.path
22	22	import numpy
	23	import sys
23	24
24	25	cliopts = []
25	26	cliopts.append(("without-openmp",None,"build without OpenMP support"))
26	27
27	28	options = FancyGetopt(option_table = cliopts)
28		args,opts = options.getopt()
	29
	30	#first read all the arguments passed to the script
	31	#we need to do this otherwise the --help commands would not work
	32	args = sys.argv[1:]
	33	try:
	34	#search the arguments for options we would like to use
	35	#get new args with the custom options stripped away
	36	args,opts = options.getopt(args)
	37	except:
	38	pass
29	39
30	40	#set default flags
31	41	without_openmp = False

63	73	e.extra_link_args = lopt[ c ]
64	74	build_ext.build_extensions(self)
65	75
	76	cmdclass = {'build_ext': build_ext_subclass}
	77
66	78	with open('README.txt') as f:
67	79	long_description = f.read()
68	80

75	87	os.path.join('xrayutilities','src','gridder3d.c')],
76	88	define_macros = user_macros)
77	89
	90	try:
	91	import sphinx
	92	from sphinx.setup_command import BuildDoc
	93
	94	class build_doc(BuildDoc):
	95	def run(self):
	96	# make sure the python path is pointing to the newly built
	97	# code so that the documentation is built on this and not a
	98	# previously installed version
	99	build = self.get_finalized_command('build')
	100	sys.path.insert(0, os.path.abspath(build.build_lib))
	101	try:
	102	sphinx.setup_command.BuildDoc.run(self)
	103	except UnicodeDecodeError:
	104	print("ERROR: unable to build documentation"
	105	" because Sphinx do not handle"
	106	" source path with non-ASCII characters. Please"
	107	" try to move the source package to another"
	108	" location (path with only ASCII characters)")
	109	sys.path.pop(0)
	110
	111	cmdclass['build_doc'] = build_doc
	112	except ImportError:
	113	pass
	114
78	115	setup(name="xrayutilities",
79		version="1.0.2",
	116	version="1.0.3",
80	117	author="Eugen Wintersberger, Dominik Kriegner",
81	118	description="package for x-ray diffraction data evaluation",
82	119	classifiers=["Topic :: Scientific/Engineering :: Physics",

95	132	requires=['numpy','scipy','matplotlib','tables'],
96	133	include_dirs = [numpy.get_include()],
97	134	ext_modules = [extmodul],
98		cmdclass = {'build_ext': build_ext_subclass },
	135	cmdclass = cmdclass,
99	136	url="http://xrayutilities.sourceforge.net",
100	137	license="GPLv2",
101	138	script_args = args

+1

-1

xrayutilities/analysis/line_cuts3d.py less more

18	18
19	19	from .. import config
20	20	from .. import experiment
21		from .. import gridder as xugridder
	21	from .. import gridder3d as xugridder
22	22
23	23	def getindex3d(x,y,z,xgrid,ygrid,zgrid):
24	24	"""

+4

-4

xrayutilities/analysis/sample_align.py less more

1774	1774	else:
1775	1775	[qx,qy,qz] = exphxrd.Ang2Q(om,tt)
1776	1776	[qxsub,qysub,qzsub] = exphxrd.Ang2Q(omalign,ttalign)
1777		params = [qysub[0],qzsub[0],0.001,0.001,psd.max(),0,0.]
1778		params,covariance = math.fit_peak2d(qy.flatten(),qz.flatten(),psd.flatten(),params,[qysub[0]-frange[0],qysub[0]+frange[0],qzsub[0]-frange[1],qzsub[0]+frange[1]],math.Gauss2d,maxfev=10000)
	1777	params = [qysub,qzsub,0.001,0.001,psd.max(),0,0.]
	1778	params,covariance = math.fit_peak2d(qy.flatten(),qz.flatten(),psd.flatten(),params,[qysub-frange[0],qysub+frange[0],qzsub-frange[1],qzsub+frange[1]],math.Gauss2d,maxfev=10000)
1779	1779	# correct params
1780	1780	params[6] = params[6]%(numpy.pi)
1781	1781	if params[5]<0 : params[5] = 0

1786	1786
1787	1787	if plot:
1788	1788	plt.figure(); plt.clf()
1789		from .. import gridder
	1789	from ..gridder2d import Gridder2D
1790	1790	from .. import utilities
1791		gridder = gridder.Gridder2D(400,400)
	1791	gridder = Gridder2D(400,400)
1792	1792	gridder(qy,qz,psd)
1793	1793	# calculate intensity which should be plotted
1794	1794	INT = utilities.maplog(gridder.gdata.transpose(),4,0)

+2

-2

xrayutilities/experiment.py less more

1125	1125	raise Exception("unknown keyword argument given: allowed are 'B': orthonormalization matrix, 'U': orientation matrix, 'mat': material object, 'dettype': string with detector type")
1126	1126
1127	1127	if "B" in kwargs:
1128		B = numpy.array(B)
	1128	B = numpy.array(kwargs['B'])
1129	1129	kwargs.pop("B")
1130	1130	elif "mat" in kwargs:
1131	1131	mat = kwargs['mat']

1135	1135	B = numpy.identity(3)
1136	1136
1137	1137	if "U" in kwargs:
1138		U = numpy.array(U)
	1138	U = numpy.array(kwargs['U'])
1139	1139	kwargs.pop("U")
1140	1140	else:
1141	1141	U = self._transform.matrix

+5

-0

xrayutilities/math/__init__.py less more

42	42	from .functions import Gauss3d
43	43	from .functions import TwoGauss2d
44	44	from .functions import Lorentz1d
	45	from .functions import Lorentz1d_der_x
	46	from .functions import Lorentz1d_der_p
45	47	from .functions import Lorentz2d
	48	from .functions import PseudoVoigt1d
46	49
47	50	from .fit import fit_peak2d
48	51	from .fit import gauss_fit
	52	from .fit import multPeakFit
	53	from .fit import multPeakPlot
49	54	from .fit import multGaussFit
50	55	from .fit import multGaussPlot

+57

-18

xrayutilities/math/fit.py less more

28	28
29	29	from .. import config
30	30	from .functions import Gauss1d,Gauss1d_der_x,Gauss1d_der_p
	31	from .functions import Lorentz1d,Lorentz1d_der_x,Lorentz1d_der_p
31	32
32	33	try:
33	34	from matplotlib import pyplot as plt

83	84	# use least-square fit
84	85	myodr.set_job(fit_type=2)
85	86
86		# # DK comment out because this command triggers a synthax error with new scipy version 2013/5/7
	87	# # DK commented out because this command triggers a synthax error with new scipy version 2013/5/7
87	88	# if config.VERBOSITY >= config.DEBUG:
88	89	# myodr.set_iprint(final=1)
89	90

156	157	return p,pcov
157	158
158	159
159		def multGaussFit(x,data,peakpos,peakwidth,dranges=None):
160		"""
161		function to fit multiple Gaussian peaks with linear background to a set of data
	160	def multGaussFit(args,*kwargs):
	161	"""
	162	convenience function to keep API stable
	163	see multPeakFit for documentation
	164	"""
	165	kwargs['peaktype']='Gaussian'
	166	return multPeakFit(args,*kwargs)
	167
	168	def multPeakFit(x,data,peakpos,peakwidth,dranges=None,peaktype='Gaussian'):
	169	"""
	170	function to fit multiple Gaussian/Lorentzian peaks with linear background to a set of data
162	171
163	172	Parameters
164	173	----------

168	177	peakwidth: initial values for the peak width
169	178	dranges: list of tuples with (min,max) value of the data ranges to use.
170	179	does not need to have the same number of entries as peakpos
	180	peaktype: type of peaks to be used: can be either 'Gaussian' or 'Lorentzian'
171	181
172	182	Returns
173	183	-------

178	188	amp: list of amplitudes of the peaks derived by the fit
179	189	background: array of background values at positions x
180	190	"""
	191	if peaktype=='Gaussian':
	192	pfunc = Gauss1d
	193	pfunc_derx = Gauss1d_der_x
	194	elif peaktype=='Lorentzian':
	195	pfunc = Lorentz1d
	196	pfunc_derx = Lorentz1d_der_x
	197	else:
	198	raise ValueError('wrong value for parameter peaktype was given')
	199
181	200	def deriv_x(p, x):
182	201	"""
183	202	function to calculate the derivative of the signal of multiple peaks and background w.r.t. the x-coordinate

190	209
191	210	# sum up peak functions contributions
192	211	for i in range(len(p)//3):
193		ldx = Gauss1d_der_x(x,p[3i],p[3i+1],p[3*i+2],0)
	212	ldx = pfunc_derx(x,p[3i],p[3i+1],p[3*i+2],0)
194	213	derx += ldx
195	214
196	215	# background contribution

214	233	# peak functions contributions
215	234	for i in range(len(p)//3):
216	235	lp = (p[3i],p[3i+1],p[3*i+2],0)
217		derp = numpy.append(derp,-2(lp[0]-x)Gauss1d(x,*lp))
218		derp = numpy.append(derp,(lp[0]-x)*2/(2lp[1]*3)Gauss1d(x,*lp))
219		derp = numpy.append(derp,Gauss1d(x,*lp)/lp[2])
220
	236	if peaktype == 'Gaussian':
	237	derp = numpy.append(derp,-2(lp[0]-x)pfunc(x,*lp))
	238	derp = numpy.append(derp,(lp[0]-x)*2/(2lp[1]*3)pfunc(x,*lp))
	239	derp = numpy.append(derp,pfunc(x,*lp)/lp[2])
	240	else: # Lorentzian
	241	derp = numpy.append(derp,4(x-lp[0]) lp[2]/lp[1]/(1+(2(x-lp[0])/lp[1])2)*2)
	242	derp = numpy.append(derp,4(lp[0]-x) lp[2]/lp[1]*2/(1+(2(x-lp[0])/lp[1])2)2)
	243	derp = numpy.append(derp,1/(1+(2(x-p[0])/p[1])*2))
	244
221	245	# background contributions
222	246	derp = numpy.append(derp,x)
223	247	derp = numpy.append(derp,numpy.ones(x.size))

238	262
239	263	# sum up peak functions
240	264	for i in range(len(p)//3):
241		lf = Gauss1d(x,p[3i],p[3i+1],p[3*i+2],0)
	265	lf = pfunc(x,p[3i],p[3i+1],p[3*i+2],0)
242	266	f += lf
243	267
244	268	# background

290	314	fit = my_odr.run()
291	315
292	316	if(config.VERBOSITY >= config.DEBUG):
293		print("XU.math.multGaussFit: fitted parameters")
	317	print("XU.math.multPeakFit: fitted parameters")
294	318	print(fit.beta)
295	319	try:
296	320	if fit.stopreason[0] not in ['Sum of squares convergence']:
297		print("XU.math.multGaussFit: fit NOT converged (%s)" %fit.stopreason[0])
	321	print("XU.math.multPeakFit: fit NOT converged (%s)" %fit.stopreason[0])
298	322	return None,None,None,None
299	323	except:
300		print("XU.math.multGaussFit: fit most probably NOT converged (%s)" %str(fit.stopreason))
	324	print("XU.math.multPeakFit: fit most probably NOT converged (%s)" %str(fit.stopreason))
301	325	return None,None,None,None
302	326	# prepare return values
303	327	fpos = fit.beta[:-2:3]

307	331
308	332	return fpos,fwidth,famp,background
309	333
310		def multGaussPlot(x,fpos,fwidth,famp,background,dranges=None,fig="xu_plot",fact=1.):
311		"""
312		function to plot multiple Gaussian peaks with linear background
	334
	335	def multGaussPlot(args,*kwargs):
	336	"""
	337	convenience function to keep API stable
	338	see multPeakPlot for documentation
	339	"""
	340	kwargs['peaktype']='Gaussian'
	341	return multPeakPlot(args,*kwargs)
	342
	343	def multPeakPlot(x,fpos,fwidth,famp,background,dranges=None,peaktype='Gaussian',fig="xu_plot",fact=1.):
	344	"""
	345	function to plot multiple Gaussian/Lorentz peaks with background values given by an array
313	346
314	347	Parameters
315	348	----------

320	353	background: array with background values
321	354	dranges: list of tuples with (min,max) value of the data ranges to use.
322	355	does not need to have the same number of entries as fpos
	356	peaktype: type of peaks to be used: can be either 'Gaussian' or 'Lorentzian'
323	357	fig: matplotlib figure number or name
324	358	fact: factor to use as multiplicator in the plot
325	359	"""
326	360
327	361	try: plt.__name__
328	362	except NameError:
329		print("XU.math.multGaussPlot: Warning: plot functionality not available")
	363	print("XU.math.multPeakPlot: Warning: plot functionality not available")
330	364	return
331	365
332	366	plt.figure(fig)

345	379
346	380	f = numpy.zeros(lx.size)
347	381	for i in range(len(fpos)):
348		lf = Gauss1d(lx,fpos[i],fwidth[i],famp[i],0)
	382	if peaktype=='Gaussian':
	383	lf = Gauss1d(lx,fpos[i],fwidth[i],famp[i],0)
	384	elif peaktype=='Lorentzian':
	385	lf = Lorentz1d(lx,fpos[i],fwidth[i],famp[i],0)
	386	else:
	387	raise ValueError('wrong value for parameter peaktype was given')
349	388	f += lf
350	389	plt.plot(lx,(lf+lb)*fact,'k:')
351	390

+56

-5

xrayutilities/math/functions.py less more

110	110	for parameter description see Gauss1d
111	111	"""
112	112
113		return 2(p[0]-x)Gauss1d(x,*p)
	113	lp = numpy.copy(p)
	114	lp[3] = 0
	115	return 2(p[0]-x)Gauss1d(x,*lp)
114	116
115	117
116	118	def Gauss1d_der_p(x,*p):

120	122
121	123	for parameter description see Gauss1d
122	124	"""
123
124		r = numpy.concatenate(( -2(p[0]-x)Gauss1d(x,*p),\
125		(p[0]-x)*2/(2p[1]*3)Gauss1d(x,*p),\
126		Gauss1d(x,*p)/p[2],\
	125	lp = numpy.copy(p)
	126	lp[3] = 0
	127	r = numpy.concatenate(( -2(p[0]-x)Gauss1d(x,*lp),\
	128	(p[0]-x)*2/(2p[1]*3)Gauss1d(x,*lp),\
	129	Gauss1d(x,*lp)/p[2],\
127	130	numpy.ones(x.shape,dtype=numpy.float) ))
128	131	r.shape = (4,) + x.shape
129	132

224	227
225	228	return g
226	229
	230	def Lorentz1d_der_x(x,*p):
	231	"""
	232	function to calculate the derivative of a Gaussian with respect to x
	233
	234	for parameter description see Lorentz1d
	235	"""
	236
	237	return 4(p[0]-x) p[2]/p[1]/(1+(2(x-p[0])/p[1])2)*2
	238
	239	def Lorentz1d_der_p(x,*p):
	240	"""
	241	function to calculate the derivative of a Gaussian with respect the
	242	parameters p
	243
	244	for parameter description see Lorentz1d
	245	"""
	246
	247	r = numpy.concatenate(( 4(x-p[0]) p[2]/p[1]/(1+(2(x-p[0])/p[1])2)*2,\
	248	4(p[0]-x) p[2]/p[1]*2/(1+(2(x-p[0])/p[1])2)2,\
	249	1/(1+(2(x-p[0])/p[1])*2),\
	250	numpy.ones(x.shape,dtype=numpy.float) ))
	251	r.shape = (4,) + x.shape
	252
	253	return r
	254
227	255	def Lorentz2d(x,y,*p):
228	256	"""
229	257	function to calculate a general two dimensional Lorentzian

248	276
249	277	g = p[5]+p[4]/(1+(2(rcen_x-xp)/p[2])2+(2(rcen_y-yp)/p[3])**2)
250	278	return g
	279
	280
	281	def PseudoVoigt1d(x,*p):
	282	"""
	283	function to calculate a pseudo Voigt function as linear combination of a Gauss and Lorentz peak
	284
	285	Parameters
	286	----------
	287	p: list of parameters of the Lorentz-function
	288	[XCEN,FWHM,AMP,BACKGROUND,ETA]
	289	ETA: 0 ...1 0 means pure Gauss and 1 means pure Lorentz
	290	x,y: coordinate(s) where the function should be evaluated
	291
	292	Returns
	293	-------
	294	the value of the PseudoVoigt described by the parameters p
	295	at position (x,y)
	296
	297	"""
	298
	299	f = p[3]+p[2] * ( p[4](1/(1+(2(x-p[0])/(p[1]/2.))*2)) + (1-p[4])numpy.exp(-numpy.log(2)((p[0]-x)/(p[1]/2.))*2) )
	300
	301	return f
251	302
252	303
253	304	def Debye1(x):

xrayutilities.pdf less more

Binary diff not shown