Commit upstream/1.7.1+git20210715.1.9ac4344 - xrayutilities

+9

-0

CHANGES.txt less more

	0	* update copyright notices from git commit history
	1	* fix code error found by linting (flake8)
	2	* CIF atom type normalization of oxidation state (issue #122)
	3	* improve documentation of PowerModel multiprocessing code (issue #121)
	4	* fix numpy-1.20 deprecation warnings
	5	* bugfix in kinematical diffraction model.
	6	* add visualization of individual layer densities (issue #107)
	7	* new coplanar_alphaf helper function
	8
0	9	v1.7.1, 2021-01-02
1	10
2	11	* harmonize dependency versions between README and setup.py

+2

-2

PKG-INFO less more

11	11	=============
12	12
13	13
14		[![Build Status](https://dev.azure.com/dominikkriegner/xrayutilities/_apis/build/status/dkriegner.xrayutilities?repoName=dkriegner%2Fxrayutilities&branchName=master)](https://dev.azure.com/dominikkriegner/xrayutilities/_build/latest?definitionId=1&repoName=dkriegner%2Fxrayutilities&branchName=master)
	14	[![Build Status](https://dev.azure.com/dominikkriegner/xrayutilities/_apis/build/status/dkriegner.xrayutilities?repoName=dkriegner%2Fxrayutilities&branchName=main)](https://dev.azure.com/dominikkriegner/xrayutilities/_build/)
15	15
16	16	xrayutilities is a collection of scripts used to analyze and simulate x-ray
17	17	diffraction data. It consists of a Python package and several routines coded

215	215	Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
216	216	Requires-Python: ~=3.6
217	217	Description-Content-Type: text/markdown
	218	Provides-Extra: fit
218	219	Provides-Extra: plot
219		Provides-Extra: fit

+1

-1

README.md less more

1	1	=============
2	2
3	3
4		[![Build Status](https://dev.azure.com/dominikkriegner/xrayutilities/_apis/build/status/dkriegner.xrayutilities?repoName=dkriegner%2Fxrayutilities&branchName=master)](https://dev.azure.com/dominikkriegner/xrayutilities/_build/latest?definitionId=1&repoName=dkriegner%2Fxrayutilities&branchName=master)
	4	[![Build Status](https://dev.azure.com/dominikkriegner/xrayutilities/_apis/build/status/dkriegner.xrayutilities?repoName=dkriegner%2Fxrayutilities&branchName=main)](https://dev.azure.com/dominikkriegner/xrayutilities/_build/)
5	5
6	6	xrayutilities is a collection of scripts used to analyze and simulate x-ray
7	7	diffraction data. It consists of a Python package and several routines coded

+2

-0

doc/source/conf.py less more

371	371	for i in range(len(lines)):
372	372	lines[i] = re.sub(r'^\s*Note:', r'.. note::', lines[i])
373	373
	374
374	375	def skip(app, what, name, obj, would_skip, options):
375	376	"""always document __init__ and __call__ functions"""
376	377	if name in ["__init__", "__call__"]:
377	378	return False
378	379	return would_skip
379	380
	381
380	382	def setup(app):
381	383	app.connect('autodoc-process-docstring', process_docstring)
382	384	app.connect("autodoc-skip-member", skip)

+4

-4

doc/source/examples.rst less more

5	5	Examples
6	6	========
7	7
8		In the following a few code-snippets are shown which should help you getting started with xrayutilities. Not all of the codes shown in the following will be run-able as stand-alone script. For fully running scripts look in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ or in the `download <https://sourceforge.net/projects/xrayutilities>`_.
	8	In the following a few code-snippets are shown which should help you getting started with xrayutilities. Not all of the codes shown in the following will be run-able as stand-alone script. For fully running scripts look in the `examples <https://github.com/dkriegner/xrayutilities/tree/main/examples>`_ or in the `download <https://sourceforge.net/projects/xrayutilities>`_.
9	9
10	10
11	11	Reading data from data files

95	95	e.Save2HDF5(h5file, group="/frelon_%04d" % i)
96	96
97	97	.. seealso::
98		the fully working example provided in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ directory perfectly suited for reading data from beamline ID01
	98	the fully working example provided in the `examples <https://github.com/dkriegner/xrayutilities/tree/main/examples>`_ directory perfectly suited for reading data from beamline ID01
99	99
100	100	Reading XRDML files
101	101	^^^^^^^^^^^^^^^^^^^

115	115
116	116
117	117	.. seealso::
118		the fully working example provided in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ directory
	118	the fully working example provided in the `examples <https://github.com/dkriegner/xrayutilities/tree/main/examples>`_ directory
119	119
120	120	Other formats
121	121	^^^^^^^^^^^^^

130	130	* support is also provided for reading of ``cif`` files from structure
131	131	databases to extract unit cell parameters as well es read data from those files (pdCIF, ESG files)
132	132
133		See the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ directory for more information and working example scripts.
	133	See the `examples <https://github.com/dkriegner/xrayutilities/tree/main/examples>`_ directory for more information and working example scripts.
134	134
135	135	Angle calculation using :class:`~xrayutilities.experiment.Experiment` and :mod:`~xrayutilities.materials` classes
136	136	-----------------------------------------------------------------------------------------------------------------

+4

-4

doc/source/simulations.rst less more

5	5	Simulation examples
6	6	===================
7	7
8		In the following a few code-snippets are shown which should help you getting started with reflectivity and diffraction simulations using xrayutilities. All simulations in xrayutilities are for layers systems and currently there are no plans to extend this to other geometries. Note that not all of the codes shown in the following will be run-able as stand-alone scripts. For fully running scripts look in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ directory in the `download <https://sourceforge.net/projects/xrayutilities>`_.
	8	In the following a few code-snippets are shown which should help you getting started with reflectivity and diffraction simulations using xrayutilities. All simulations in xrayutilities are for layers systems and currently there are no plans to extend this to other geometries. Note that not all of the codes shown in the following will be run-able as stand-alone scripts. For fully running scripts look in the `examples <https://github.com/dkriegner/xrayutilities/tree/main/examples>`_ directory in the `download <https://sourceforge.net/projects/xrayutilities>`_.
9	9
10	10	Building Layer stacks for simulations
11	11	-------------------------------------

295	295	Fitting of diffraction data
296	296	~~~~~~~~~~~~~~~~~~~~~~~~~~~
297	297
298		All diffraction models can be embedded into the :class:`~xrayutilities.simpack.fit.FitModel` class, which is suitable to refine the model parameters. Below (and in the `examples <https://github.com/dkriegner/xrayutilities/tree/master/examples>`_ directory) a runnable script is shown which shows the fitting for a pseudomorphic InMnAs epilayer on InAs(001). The fitting is performed using the `lmfit <https://lmfit.github.io/lmfit-py/>`_ Python package which needs to be installed when you want to use this fitting function. As one can see below the :func:`~xrayutilities.simpack.FitModel.set_param_hint` function can be used to set up the respective fit parameters including their boundaries and possible correlation with other parameters of the model. It should be equally possible to fit more complex layer structures, however, I expect that one needs to adjust manually the starting parameters to yield something very reasonable. Since this capabilities are rather new please report back any success/problems you have with this via the mailing list.
	298	All diffraction models can be embedded into the :class:`~xrayutilities.simpack.fit.FitModel` class, which is suitable to refine the model parameters. Below (and in the `examples <https://github.com/dkriegner/xrayutilities/tree/main/examples>`_ directory) a runnable script is shown which shows the fitting for a pseudomorphic InMnAs epilayer on InAs(001). The fitting is performed using the `lmfit <https://lmfit.github.io/lmfit-py/>`_ Python package which needs to be installed when you want to use this fitting function. As one can see below the :func:`~xrayutilities.simpack.FitModel.set_param_hint` function can be used to set up the respective fit parameters including their boundaries and possible correlation with other parameters of the model. It should be equally possible to fit more complex layer structures, however, I expect that one needs to adjust manually the starting parameters to yield something very reasonable. Since this capabilities are rather new please report back any success/problems you have with this via the mailing list.
299	299
300	300	.. code-block:: python
301	301	:linenos:

376	376	# pm.close() # after end-of-use
377	377
378	378
379		Note that in MS windows you need to encapsulate this code into a dummy function to allow for the multiprocessing module to work correctly. The code then must look like::
	379	Note that in MS windows and macOS you need to encapsulate this code into a dummy function to allow for the multiprocessing module to work correctly. See the `Python documentation <https://docs.python.org/3/library/multiprocessing.html#the-spawn-and-forkserver-start-methods>`_ for details. The code then must look like::
380	380
381	381	import numpy
382	382	import xrayutilities as xu

393	393	pm.close()
394	394
395	395	if __name__ == '__main__':
396		freeze_support()
	396	freeze_support() # only required on MS Windows
397	397	main()

+9

-2

examples/simpack_powdermodel.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2017 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2017-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import multiprocessing
18	18	import os

24	24
25	25
26	26	def main():
27		"""dummy main function to enable multiprocessing on windows"""
	27	"""
	28	dummy main function to enable multiprocessing on Windows and macOS.
	29	This is required to avoid starting of the multiprocessing code upon import
	30	of the script and is connected with the used multiprocessing start method.
	31
	32	See also:
	33	https://docs.python.org/3/library/multiprocessing.html#the-spawn-and-forkserver-start-methods
	34	"""
28	35	mpl.rcParams['font.size'] = 16.0
29	36	mpl.rcParams['lines.linewidth'] = 2.0
30	37

+5

-2

examples/simpack_xrr_effectivedensityslicing.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2020-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16	# Copyright (C) 2020 Mike Moron <mike.moron@tu-dortmund.de>
17	17
18	18	import numpy as np

37	37
38	38	# conventional X-ray reflectivity modelling
39	39	m = xu.simpack.SpecularReflectivityModel(ls)
40		pos, eldens = m.densityprofile(500)
	40	pos, eldens, layer_eldens = m.densityprofile(500, individual_layers=True)
	41
41	42
42	43	# slice the layerstack into an Amorphous sublayer at every 0.1 angstrom.
43	44	# at the top a vacuum layer is added

59	60	fig = plt.figure()
60	61	ax = fig.add_subplot(111)
61	62	ax.plot(pos, eldens, '.-', label='conventional')
	63	for i in range(len(layer_eldens)):
	64	ax.plot(pos, layer_eldens[i], ':')
62	65	ax.plot(spos, seldens, '.-', label='sliced') # arbitrary shift for vis.
63	66	ax.legend()
64	67	ax.set_xlabel(r'z-position')

+2

-2

examples/xrayutilities_hotpixelkill_variant.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2013 Raphael Grifone <raphael.grifone@esrf.fr>
16		# Copyright (C) 2013 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2013-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17
18	18	"""
19	19	The function below is a modification of the hotpixelkill function included in

50	50	e = xu.io.EDFFile(f)
51	51	ccdraw = e.data
52	52	if len(ccdavg) == 0:
53		ccdavg = ccdraw.astype(numpy.float)
	53	ccdavg = ccdraw.astype(float)
54	54	else:
55	55	ccdavg += ccdraw
56	56	n += 1

+2

-2

examples/xrayutilities_read_spec.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2012 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	Example script to show how to use xrayutilities to read and plot

54	54	# correction
55	55	normalizer_detcorr = xu.IntensityNormalizer(
56	56	"MCA", mon="Monitor", time="Seconds",
57		absfun=lambda d: d["detcorr"] / d["psd2"].astype(numpy.float))
	57	absfun=lambda d: d["detcorr"] / d["psd2"].astype(float))
58	58
59	59	# substrate material used for Bragg peak calculation to correct for
60	60	# experimental offsets

+1

-1

lib/xrayutilities/__init__.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2009-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17
18	18	"""
19	19	xrayutilities is a Python package for assisting with x-ray diffraction

+1

-1

lib/xrayutilities/analysis/line_cuts.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2018-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2011-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import numpy
18	18

+2

-2

lib/xrayutilities/analysis/sample_align.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2011-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2011-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	functions to help with experimental alignment during experiments, especially

151	151	rad = radians(x)
152	152	p2 = math.radians(p[2])
153	153	r = numpy.concatenate([degrees(sin(rad)) / cos(rad - p2),
154		numpy.ones(x.shape, dtype=numpy.float),
	154	numpy.ones(x.shape, dtype=float),
155	155	- math.degrees(p[0]) * sin(rad) /
156	156	cos(rad - p2) ** 2 * sin(rad - p2)])
157	157	r.shape = (3,) + x.shape

+1

-1

lib/xrayutilities/exception.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2010 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2010-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	xrayutilities derives its own exceptions which are raised

+7

-7

lib/xrayutilities/experiment.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009-2010 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2009-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17	# Copyright (C) 2012 Tanja Etzelstorfer <tanja.etzelstorfer@jku.at>
18	18
19	19	"""

484	484	flag to tell if angles are passed as degree (default: True)
485	485	sampledis : tuple or list or array-like
486	486	sample displacement vector in relative units of the detector
487		distance (default: (0, 0, 0))
	487	distance. Applies to parallal beam geometry. (default: (0, 0, 0))
488	488	"""
489	489	flags = 0
490	490	if self._has_translations:

564	564	flag to tell if angles are passed as degree (default: True)
565	565	sampledis : tuple or list or array-like
566	566	sample displacement vector in relative units of the detector
567		distance (default: (0, 0, 0))
	567	distance. Applies to parallal beam geometry. (default: (0, 0, 0))
568	568
569	569	Returns
570	570	-------

768	768	flag to tell if angles are passed as degree (default: True)
769	769	sampledis : tuple or list or array-like
770	770	sample displacement vector in relative units of the detector
771		distance (default: (0, 0, 0))
	771	distance. Applies to parallal beam geometry. (default: (0, 0, 0))
772	772
773	773	Returns
774	774	-------

1018	1018	flag to tell if angles are passed as degree (default: True)
1019	1019	sampledis : tuple or list or array-like
1020	1020	sample displacement vector in relative units of the detector
1021		distance (default: (0, 0, 0))
	1021	distance. Applies to parallal beam geometry. (default: (0, 0, 0))
1022	1022
1023	1023
1024	1024	Returns

1575	1575	x-ray energy in eV (default: converted self._wl)
1576	1576	deg : bool, optional
1577	1577	flag to tell if angles are passed as degree (default: True)
1578		sampledis : tuple, list or array-like, optional
	1578	sampledis : tuple or list or array-like
1579	1579	sample displacement vector in relative units of the detector
1580		distance (default: (0, 0, 0))
	1580	distance. Applies to parallal beam geometry. (default: (0, 0, 0))
1581	1581
1582	1582	Returns
1583	1583	-------

+2

-2

lib/xrayutilities/gridder.py less more

15	15	# Copyright (C) 2009-2010, 2013
16	16	# Eugen Wintersberger <eugen.wintersberger@desy.de>
17	17	# Copyright (C) 2009 Mario Keplinger <mario.keplinger@jku.at>
18		# Copyright (C) 2009-2017 Dominik Kriegner <dominik.kriegner@gmail.com>
	18	# Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
19	19
20	20	import abc
21	21

164	164	"""
165	165	prepare array for passing to c-code
166	166	"""
167		if isinstance(a, (list, tuple, numpy.float, numpy.int)):
	167	if isinstance(a, (list, tuple, float, int)):
168	168	a = numpy.asarray(a)
169	169	return a.reshape(a.size)
170	170

+3

-3

lib/xrayutilities/gridder2d.py less more

15	15	# Copyright (C) 2009-2010, 2013
16	16	# Eugen Wintersberger <eugen.wintersberger@desy.de>
17	17	# Copyright (C) 2009 Mario Keplinger <mario.keplinger@jku.at>
18		# Copyright (C) 2009-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	18	# Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
19	19
20	20	import numpy
21	21

250	250	for i in range(self.nx):
251	251	for j in range(self.ny):
252	252	self._gdata[i, j] = []
253		self._gnorm = numpy.zeros((self.nx, self.ny), dtype=numpy.int)
	253	self._gnorm = numpy.zeros((self.nx, self.ny), dtype=int)
254	254
255	255	def Clear(self):
256	256	self._allocate_memory()

284	284
285	285	# perform gridding this should be moved to native code if possible
286	286	def gindex(x, min, delt):
287		return numpy.round((x - min) / delt).astype(numpy.int)
	287	return numpy.round((x - min) / delt).astype(int)
288	288
289	289	xdelta = delta(self.xmin, self.xmax, self.nx)
290	290	ydelta = delta(self.ymin, self.ymax, self.ny)

+1

-1

lib/xrayutilities/gridder3d.py less more

15	15	# Copyright (C) 2009-2010, 2013
16	16	# Eugen Wintersberger <eugen.wintersberger@desy.de>
17	17	# Copyright (C) 2009 Mario Keplinger <mario.keplinger@jku.at>
18		# Copyright (C) 2009-2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	18	# Copyright (C) 2009-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
19	19
20	20	import numpy
21	21

+1

-1

lib/xrayutilities/io/cbf.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2013, 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	# module for handling files stored in the CBF data format
18	18

+2

-2

lib/xrayutilities/io/desy_tty08.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2013-2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17
18	18	"""

78	78	def ReadMCA(self):
79	79	self.mca = numpy.empty((len(self.mca_files),
80	80	numpy.loadtxt(self.mca_files[0]).shape[0]),
81		dtype=numpy.float)
	81	dtype=float)
82	82	for i in range(len(self.mca_files)):
83	83	mcadata = numpy.loadtxt(self.mca_files[i])
84	84

+1

-1

lib/xrayutilities/io/edf.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009-2010 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2010-2012,2014-2015
	16	# Copyright (C) 2010-2012,2014-2019
17	17	# Dominik Kriegner <dominik.kriegner@gmail.com>
18	18	# Copyright (C) 2012 Tanja Etzelstorfer <tanja.etzelstorfer@jku.at>
19	19

+1

-1

lib/xrayutilities/io/filedir.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import glob
18	18	import os.path

+1

-1

lib/xrayutilities/io/ill_numor.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	module for reading ILL data files (station D23): numor files

+1

-1

lib/xrayutilities/io/imagereader.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2012-2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import time

+2

-1

lib/xrayutilities/io/pdcif.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import copy
18	18	import re

108	108	loopheader = []
109	109	numOfEntries = -1
110	110	multiline = None
	111	label = None
111	112
112	113	while True:
113	114	line = fh.readline().decode('ascii')

+1

-1

lib/xrayutilities/io/rigaku_ras.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015-2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17
18	18	"""

+2

-2

lib/xrayutilities/io/seifert.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2009-2013 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17
18	18	"""
19	19	a set of routines to convert Seifert ASCII files to HDF5

267	267	self.data.append(tmplist)
268	268
269	269	# in the end we convert the data list to a numeric array
270		self.data = numpy.array(self.data, dtype=numpy.float)
	270	self.data = numpy.array(self.data, dtype=float)
271	271	for key in self.axispos:
272	272	self.axispos[key] = numpy.array(self.axispos[key])
273	273

+3

-2

lib/xrayutilities/io/spec.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009-2010 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2009-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2009-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
	17	# Copyright (C) 2019 Daniel Schick <schick.daniel@gmail.com>
17	18
18	19	"""
19	20	a class for observing a SPEC data file

510	511
511	512	# write the initial motor positions as attributes
512	513	for k in self.init_motor_pos:
513		g.attrs[k] = numpy.float(self.init_motor_pos[k])
	514	g.attrs[k] = float(self.init_motor_pos[k])
514	515
515	516	# if scan contains MCA data write also MCA parameters
516	517	g.attrs['has_mca'] = self.has_mca

+1

-1

lib/xrayutilities/io/spectra.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009-2010 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2009-2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2009-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17
18	18	"""
19	19	module to handle spectra data

+1

-1

lib/xrayutilities/materials/__init__.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2010-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2010-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17
18	18	from . import elements
19	19	from .atom import Atom

+1

-0

lib/xrayutilities/materials/_create_database.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
	15	# Copyright (C) 2009-2012 Eugen Wintersberger <eugen.wintersberger@desy.de>
15	16	# Copyright (C) 2012-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	17	"""
17	18	script to create the HDF5 database from the raw data of XOP.

+1

-1

lib/xrayutilities/materials/atom.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2009-2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	module containing the Atom class which handles the database access for atomic

+8

-2

lib/xrayutilities/materials/cif.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2010-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2010-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import copy
18	18	import io

217	217	def get_element(cifstring):
218	218	el = re.sub(r"['\"]", r"", cifstring)
219	219	if '+' in el or '-' in el:
	220	# add oxidation number if not present
	221	for sign in ('+', '-'):
	222	if sign in el:
	223	if not el[el.index(sign)-1].isdigit():
	224	signidx = el.index(sign)
	225	el = el[:signidx] + '1' + el[signidx:]
	226	# replace special characters
220	227	for r, o in zip(('dot', 'p', 'm'), ('.', '+', '-')):
221		# move special character to last position
222	228	el = el.replace(o, r)
223	229	else:
224	230	el = re.sub(r"([0-9])", r"", el)

+1

-1

lib/xrayutilities/materials/elements.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2010-2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2010-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17
18	18	from .atom import Atom
19	19

+1

-1

lib/xrayutilities/materials/heuslerlib.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2018 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2018-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	implement convenience functions to define Heusler materials.

+1

-1

lib/xrayutilities/materials/plot.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2018 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2018-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import math
18	18	from math import pi

+1

-1

lib/xrayutilities/materials/predefined_materials.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2013-2017 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import numpy
18	18

+2

-2

lib/xrayutilities/materials/spacegrouplattice.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2017-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2017-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16	"""
17	17	module handling crystal lattice structures. A SGLattice consists of a space
18	18	group number and the position of atoms specified as Wyckoff positions along

1268	1268	# check all atomic species seperately
1269	1269	for el in elements:
1270	1270	catoms = list(filter(lambda at: at[0] == el, atoms))
1271		found = numpy.zeros(len(catoms), dtype=numpy.bool)
	1271	found = numpy.zeros(len(catoms), dtype=bool)
1272	1272	# see if atomic positions fit to Wyckoff positions
1273	1273	for k, wyckpos in wp[sgrp].items():
1274	1274	num = int(k[:-1])

+1

-1

lib/xrayutilities/materials/wyckpos.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2018-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2017-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	__all__ = ["RangeDict", "eqhkl_default", "eqhkl_custom", "wp"]
18	18

+1

-1

lib/xrayutilities/math/__init__.py less more

13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15	15	# Copyright (C) 2009 Eugen Wintersberger <eugen.wintersberger@desy.de>
16		# Copyright (C) 2010-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	# Copyright (C) 2010-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17
18	18	from .algebra import solve_quartic
19	19	from .fit import (fit_peak2d, gauss_fit, linregress, multPeakFit, multPeakPlot,

+8

-8

lib/xrayutilities/math/algebra.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016-2018 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	module providing analytic algebraic functions not implemented in scipy or any

77	77	t36 = 16 * t17 * t27
78	78	t37 = 144 * t07 * t12 * t17
79	79	t30 = t26 + t28 + t29 - t35 - t36 - t37
80		t31 = t30.astype(numpy.complex)**(1./2)
	80	t31 = t30.astype(complex)**(1./2)
81	81	t32 = (t24 * t31) / 18
82	82	t34 = (4 * t07 * t17) / 3
83	83	t33 = t22 + t23 + t32 - t34
84		t38 = 1 / t33.astype(numpy.complex)**(1./6)
	84	t38 = 1 / t33.astype(complex)**(1./6)
85	85	t39 = t33**(1./3)
86	86	t40 = 12 * a0 * t01
87	87	t41 = t33**(2./3)

91	91	t47 = (9 * t14 * t15) / 64
92	92	t48 = 3 * a3 * a1 * t04
93	93	t44 = t08 + t40 + t42 + t43 - t46 - t47 - t48
94		t45 = t44.astype(numpy.complex)**(1./2)
	94	t45 = t44.astype(complex)**(1./2)
95	95	t49 = 6.**(1./2)
96	96	t50 = 27 * t12
97	97	t51 = 2 * t07 * t08
98	98	t52 = 3 * t24 * t31
99	99	t62 = 72 * t07 * t17
100	100	t53 = t50 + t51 + t52 - t62
101		t54 = t53.astype(numpy.complex)**(1./2)
	101	t54 = t53.astype(complex)**(1./2)
102	102	t55 = 3 * t03 * t49 * t54
103	103	t59 = t08 * t45
104	104	t60 = 12 * t17 * t45
105	105	t61 = 9 * t41 * t45
106	106	t63 = 12 * t07 * t39 * t45
107	107	t56 = t55 - t59 - t60 - t61 - t63
108		t57 = t56.astype(numpy.complex)**(1./2)
109		t58 = 1. / t44.astype(numpy.complex)**(1./4)
	108	t57 = t56.astype(complex)**(1./2)
	109	t58 = 1. / t44.astype(complex)**(1./4)
110	110	t64 = (t38 * t45) / 6
111	111	t65 = - t55 - t59 - t60 - t61 - t63
112		t66 = t65.astype(numpy.complex)**(1./2)
	112	t66 = t65.astype(complex)**(1./2)
113	113
114	114	return (-(a3 * t01) / 4 - (t38 * t45) / 6 - (t38 * t57 * t58) / 6,
115	115	(t38 * t57 * t58) / 6 - (t38 * t45) / 6 - (a3 * t01) / 4,

+2

-2

lib/xrayutilities/math/fit.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2012-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16	"""
17	17	module with a function wrapper to scipy.optimize.leastsq
18	18	for fitting of a 2D function to a peak or a 1D Gauss fit with

649	649	if fit.stopreason[0] not in ['Sum of squares convergence']:
650	650	print("XU.math.multPeakFit: fit NOT converged (%s)"
651	651	% fit.stopreason[0])
652		return Nono, None, None, None
	652	return None, None, None, None
653	653	except IndexError:
654	654	print("XU.math.multPeakFit: fit most probably NOT converged (%s)"
655	655	% str(fit.stopreason))

+4

-4

lib/xrayutilities/math/functions.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2012-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	module with several common function needed in xray data analysis

85	85	dataout = data.copy()
86	86
87	87	mean = (data[:-2] + data[2:]) / 2.
88		mask = numpy.zeros_like(data[1:-1], dtype=numpy.bool)
	88	mask = numpy.zeros_like(data[1:-1], dtype=bool)
89	89	if threshold:
90	90	mask = numpy.logical_or(
91	91	mask, numpy.logical_or(data[1:-1] * threshold < mean,

182	182	r = numpy.vstack((- (p[0] - x) / p[1]*2 Gauss1d(x, *lp),
183	183	(p[0] - x) 2 / (p[1] 3) * Gauss1d(x, *lp),
184	184	Gauss1d(x, *lp) / p[2],
185		numpy.ones(x.shape, dtype=numpy.float)))
	185	numpy.ones(x.shape, dtype=float)))
186	186
187	187	return r
188	188

320	320	8 * p[2] * p[1] * (x-p[0])**2 /
321	321	(4p[0]2 - 8p[0]x + p[1]2 + 4x2) 2,
322	322	1 / (1 + (2 * (x - p[0]) / p[1]) ** 2),
323		numpy.ones(x.shape, dtype=numpy.float)))
	323	numpy.ones(x.shape, dtype=float)))
324	324	return r
325	325
326	326

+1

-1

lib/xrayutilities/math/misc.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016-2018 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import fractions
18	18	import math

+1

-1

lib/xrayutilities/mpl_helper.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016-2017 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2017-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16	"""
17	17	Defines new matplotlib Sqrt scale which further allows for negative values by
18	18	using the sign of the original value as sign of the plotted value.

+6

-6

lib/xrayutilities/normalize.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2010-2011 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2010-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	module to provide functions that perform block averaging

235	235	Examples
236	236	--------
237	237	>>> detcorr = IntensityNormalizer("MCA", time="Seconds",
238		>>> absfun=lambda d: d["PSDCORR"]/d["PSD"].astype(numpy.float))
	238	>>> absfun=lambda d: d["PSDCORR"]/d["PSD"].astype(float))
239	239	"""
240	240	valid_kwargs = {'mon': 'monitor field name',
241	241	'time': 'count time field/value',

385	385	sets the flatfield of the detector
386	386	"""
387	387	if isinstance(flatf, (list, tuple, numpy.ndarray)):
388		self._flatfield = numpy.array(flatf, dtype=numpy.float)
	388	self._flatfield = numpy.array(flatf, dtype=float)
389	389	self._flatfieldav = numpy.mean(self._flatfield[
390	390	self._flatfield.nonzero()])
391	391	self._flatfield[self.flatfield < 1.e-5] = 1.0

411	411	sets the darkfield of the detector
412	412	"""
413	413	if isinstance(darkf, (list, tuple, numpy.ndarray)):
414		self._darkfield = numpy.array(darkf, dtype=numpy.float)
	414	self._darkfield = numpy.array(darkf, dtype=float)
415	415	self._darkfieldav = numpy.mean(self._darkfield)
416	416	elif isinstance(darkf, type(None)):
417	417	self._darkfield = None

450	450	else:
451	451	rawdata = data[self._det]
452	452
453		corrint = numpy.zeros(rawdata.shape, dtype=numpy.float)
	453	corrint = numpy.zeros(rawdata.shape, dtype=float)
454	454
455	455	# set needed variables
456	456	# monitor intensity

527	527	corrint = (corrint / self._flatfield[numpy.newaxis, :] *
528	528	self._flatfieldav)
529	529
530		elif len(rawdata.shape) == 2 and isinstance(c, numpy.float):
	530	elif len(rawdata.shape) == 2 and isinstance(c, float):
531	531	# single 2D detector frame
532	532	corrint = rawdata * c
533	533

+12

-15

lib/xrayutilities/q2ang_fit.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	Module provides functions to convert a q-vector from reciprocal space to

58	58	bounds to be handed over to the scipy.minimize routine. The function
59	59	will expand fixed values to two equal bounds
60	60	constraints, list
61		list of equivility constraints for fixed values
	61	list of equality constraints for fixed values
62	62	"""
63	63	lb = []
64	64	ub = []

69	69	lb.append(b[0])
70	70	ub.append(b[1])
71	71	elif len(b) == 1:
72		# due to a bug in scipy >= 1.5.0 we need to allow a small
73		# variation
74		lb.append(b[0] - config.EPSILON)
75		ub.append(b[0] + config.EPSILON)
76		# to really fix the parameter we create an equivalent
77		# constraint; see scipy/scipy#12433
	72	# upper = lower bound needs an equality constraint.
	73	lb.append(-numpy.inf)
	74	ub.append(numpy.inf)
	75	# see scipy/scipy#12433
78	76	constraints.append(dict(type='eq',
79	77	fun=lambda x, j=j, v=b[0]: x[j] - v,
80	78	# lambda j=j to bind variable by value

82	80	else:
83	81	raise InputError('bound values must have two or one elements')
84	82	elif isinstance(b, numbers.Number):
85		# due to a bug in scipy >= 1.5.0 we need to allow a small variation
86		lb.append(b - config.EPSILON)
87		ub.append(b + config.EPSILON)
88		# to really fix the parameter we create an equivalent
89		# constraint; see scipy/scipy#12433
	83	# upper = lower bound needs an equality constraint.
	84	lb.append(-numpy.inf)
	85	ub.append(numpy.inf)
	86	# see scipy/scipy#12433
90	87	constraints.append(dict(type='eq',
91	88	fun=lambda x, j=j, v=b: x[j] - v,
92	89	# lambda j=j to bind variable by value
93	90	))
94	91	elif b is None:
95		lb.append(-np.inf)
96		ub.append(np.inf)
	92	lb.append(-numpy.inf)
	93	ub.append(numpy.inf)
97	94	else:
98	95	raise InputError('bound value is of invalid type (%s)' % type(b))
99	96

+2

-2

lib/xrayutilities/simpack/__init__.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16	"""
17	17	simulation subpackage of xrayutilities.
18	18

28	28	DarwinModelAlloy, DarwinModelGaInAs001,
29	29	DarwinModelSiGe001, GradedBuffer)
30	30	from .fit import FitModel
31		from .helpers import coplanar_alphai, get_qz
	31	from .helpers import coplanar_alphaf, coplanar_alphai, get_qz
32	32	from .models import (DiffuseReflectivityModel, DynamicalModel,
33	33	DynamicalReflectivityModel, KinematicalModel,
34	34	KinematicalMultiBeamModel, LayerModel, Model,

+4

-4

lib/xrayutilities/simpack/darwin_theory.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16	import abc
17	17	import collections.abc
18	18	import copy

207	207	Ih = {'S': numpy.zeros(len(self.qz)), 'P': numpy.zeros(len(self.qz))}
208	208	geomfact = heaviside(self.alphai) * heaviside(self.alphaf)
209	209	for pol in self.get_polarizations():
210		r, rbar, t = (numpy.zeros(self.npoints, dtype=numpy.complex),
211		numpy.zeros(self.npoints, dtype=numpy.complex),
212		numpy.ones(self.npoints, dtype=numpy.complex))
	210	r, rbar, t = (numpy.zeros(self.npoints, dtype=complex),
	211	numpy.zeros(self.npoints, dtype=complex),
	212	numpy.ones(self.npoints, dtype=complex))
213	213	for nrep, subml in ml:
214	214	r, rbar, t = self._recur_sim(nrep, subml, r, rbar, t, pol)
215	215	self.r, self.rbar, self.t = r, rbar, t

+54

-14

lib/xrayutilities/simpack/helpers.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import numpy
18	18
19	19	from .. import config, utilities
20	20
21	21
22		def coplanar_alphai(qx, qz, en='config'):
	22	def coplanar_alphai(qx, qz, en='config', nan_Laue=False):
23	23	"""
24		calculate coplanar incidence angle from knowledge of the qx and qz
25		coordinates
	24	calculate coplanar incidence angle from knowledge of the qx (inplane) and
	25	qz (out of plane) coordinates
26	26
27	27	Parameters
28	28	----------

32	32	out of plane momentum transfer component
33	33	en : float or str, optional
34	34	x-ray energy (eV). By default the value from the config is used.
	35	nan_Laue : bool, optional
	36	set output points inside the Laue zone to 'nan'. default: False
35	37
36	38	Returns
37	39	-------
38	40	alphai : array-like
39		the incidence angle in degree. points in the Laue zone are set to
	41	the incidence angle in degree
	42	"""
	43	if isinstance(en, str) and en == 'config':
	44	en = utilities.energy(config.ENERGY)
	45	k = 2 * numpy.pi / utilities.en2lam(en)
	46	th = numpy.arcsin(numpy.sqrt(qx2 + qz2) / (2 * k))
	47	ai = numpy.arctan2(qx, qz) + th
	48	if nan_Laue:
	49	if isinstance(ai, numpy.ndarray): # remove positions in Laue zone
	50	ai[qz < numpy.sqrt(2 * qx * k - qx**2)] = numpy.nan
	51	else:
	52	if qz < numpy.sqrt(2 * qx * k - qx**2):
	53	ai = numpy.nan
	54	return numpy.degrees(ai)
	55
	56
	57	def coplanar_alphaf(qx, qz, en='config', nan_Laue=False):
	58	"""
	59	calculate coplanar exit angle from knowledge of the qx (inplane) and qz
	60	(out of plane) coordinates
	61
	62	Parameters
	63	----------
	64	qx : array-like
	65	inplane momentum transfer component
	66	qz : array-like
	67	out of plane momentum transfer component
	68	en : float or str, optional
	69	x-ray energy (eV). By default the value from the config is used.
	70	nan_Laue : bool, optional
	71	set output points inside the Laue zone to 'nan'. default: False
	72
	73	Returns
	74	-------
	75	alphaf : array-like
	76	the exit angle in degree. points in the Laue zone are set to
40	77	'nan'.
41	78	"""
42	79	if isinstance(en, str) and en == 'config':
43	80	en = utilities.energy(config.ENERGY)
44	81	k = 2 * numpy.pi / utilities.en2lam(en)
45	82	th = numpy.arcsin(numpy.sqrt(qx2 + qz2) / (2 * k))
46		ai = numpy.arctan2(qx, qz) + th
47		if isinstance(ai, numpy.ndarray): # remove positions in Laue zone
48		ai[qz < numpy.sqrt(2 * qx * k - qx**2)] = numpy.nan
49		else:
50		if qz < numpy.sqrt(2 * qx * k - qx**2):
51		ai = numpy.nan
52		return numpy.degrees(ai)
	83	af = th - numpy.arctan2(qx, qz)
	84	if nan_Laue:
	85	if isinstance(af, numpy.ndarray): # remove positions in Laue zone
	86	af[qz < numpy.sqrt(2 * qx * k - qx**2)] = numpy.nan
	87	else:
	88	if qz < numpy.sqrt(2 * qx * k - qx**2):
	89	af = numpy.nan
	90	return numpy.degrees(af)
53	91
54	92
55	93	def get_qz(qx, alphai, en='config'):

69	107	Returns
70	108	-------
71	109	array-like
72		the qz position for the given incidence angle
	110	the qz position for the given incidence angle. The output is nan in
	111	case the inplane momentum transfer can not be reached.
73	112	"""
74	113	if isinstance(en, str) and en == 'config':
75	114	en = utilities.energy(config.ENERGY)
76	115	k = 2 * numpy.pi / utilities.en2lam(en)
77	116	ai = numpy.radians(alphai)
78		return numpy.sqrt(k*2 - (qx + k numpy.cos(ai))*2) + k numpy.sin(ai)
	117	qz = numpy.sqrt(k*2 - (qx + k numpy.cos(ai))*2) + k numpy.sin(ai)
	118	return qz

+39

-26

lib/xrayutilities/simpack/models.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import abc
18	18	import copy

327	327	domega = numpy.arctan2(qinp, qz)
328	328	alphai, alphaf = (theta + domega, theta - domega)
329	329	# calculate structure factors
330		f = numpy.empty((len(self.lstack), len(qz)), dtype=numpy.complex)
331		fhkl = numpy.empty(len(self.lstack), dtype=numpy.complex)
	330	f = numpy.empty((len(self.lstack), len(qz)), dtype=complex)
	331	fhkl = numpy.empty(len(self.lstack), dtype=complex)
332	332	for i, l in enumerate(self.lstack):
333	333	m = l.material
334	334	fhkl[i] = m.StructureFactor(m.Q(*hkl), en=self.energy) /\

336	336	f[i, :] = m.StructureFactorForQ(qv, en0=self.energy) /\
337	337	m.lattice.UnitCellVolume()
338	338
339		E = numpy.zeros(len(qz), dtype=numpy.complex)
	339	E = numpy.zeros(len(qz), dtype=complex)
340	340	return rel, alphai, alphaf, f, fhkl, E, t
341	341
342	342	def _get_qz(self, qz, alphai, alphaf, chi0, absorption, refraction):
343	343	k = self.exp.k0
344		q = qz.astype(numpy.complex)
	344	q = qz.astype(complex)
345	345	if absorption and not refraction:
346	346	q += 1j * k * numpy.imag(chi0) / \
347	347	numpy.sin((alphai + alphaf) / 2)

398	398	if l.thickness == numpy.inf:
399	399	E += fhkl[i] * numpy.exp(-1j * z[i] * q) / (1j * q)
400	400	else:
401		E += - fhkl[i] * numpy.exp(-1j * q * z[i]) * \
	401	E += fhkl[i] * numpy.exp(-1j * q * z[i]) * \
402	402	(1 - numpy.exp(1j * q * l.thickness)) / (1j * q)
403	403
404	404	wf = numpy.sqrt(heaviside(ai) * heaviside(af) * rel**2 /

668	668	# deviation of the incident beam from the kinematical maximum
669	669	eta = numpy.radians(alphai) - thetaB - asym
670	670
	671	xs = None # avoid linting error in code below
671	672	for pol in self.get_polarizations():
672		x = numpy.zeros(len(alphai), dtype=numpy.complex)
	673	x = numpy.zeros(len(alphai), dtype=complex)
673	674	for i, l in enumerate(self.lstack):
674	675	beta = (2 * eta * numpy.sin(2 * thetaB) +
675	676	self.chi0[i] * (1 - gammah / gamma0) -

770	771	ah[mask] = numpy.arcsin(pp[mask])
771	772
772	773	nal = len(ai)
	774	Ps = None # make linter happy
773	775	for pol in self.get_polarizations():
774	776	if pol == 'S':
775	777	CC = numpy.ones(nal)

779	781	if config.VERBOSITY >= config.INFO_ALL:
780	782	print('XU.DynamicalModel: calc. %s-polarization...' % (pol))
781	783
782		M = numpy.zeros((nal, 4, 4), dtype=numpy.complex)
	784	M = numpy.zeros((nal, 4, 4), dtype=complex)
783	785	for j in range(4):
784	786	M[:, j, j] = numpy.ones(nal)
785	787

794	796	X = solve_quartic(A4, A3, A2, A1, A0)
795	797	X = numpy.asarray(X).T
796	798
797		kz = numpy.zeros((nal, 4), dtype=numpy.complex)
	799	kz = numpy.zeros((nal, 4), dtype=complex)
798	800	kz[:, :2] = X[numpy.imag(X) <= 0].reshape(nal, 2)
799	801	kz[:, 2:] = X[numpy.imag(X) > 0].reshape(nal, 2)
800	802
801		P = numpy.zeros((nal, 4, 4), dtype=numpy.complex)
802		phi = numpy.zeros((nal, 4, 4), dtype=numpy.complex)
	803	P = numpy.zeros((nal, 4, 4), dtype=complex)
	804	phi = numpy.zeros((nal, 4, 4), dtype=complex)
803	805	c = ((Kix2)[:, numpy.newaxis] + kz2 - kc[jL]2) / k2 /\
804	806	self.chimh['S'][jL] / CC[:, numpy.newaxis]
805	807	if jL > 0:

827	829	numpy.einsum('...ij,...jk', M, R), phi)
828	830	Ps = numpy.copy(P)
829	831
830		B = numpy.zeros((nal, 4, 4), dtype=numpy.complex)
	832	B = numpy.zeros((nal, 4, 4), dtype=complex)
831	833	B[..., :2] = M[..., :2]
832	834	B[:, 0, 2] = -numpy.ones(nal)
833	835	B[:, 1, 3] = -numpy.ones(nal)

951	953	else:
952	954	shape = numpy.ones(np)
953	955
954		ETs = numpy.ones(np, dtype=numpy.complex)
955		ERs = numpy.zeros(np, dtype=numpy.complex)
	956	ETs = numpy.ones(np, dtype=complex)
	957	ERs = numpy.zeros(np, dtype=complex)
956	958	ks = -self.exp.k0 * numpy.sqrt(sai*2 - 2 cd[0] * rho[0])
957	959
958	960	for i in range(ns):

972	974	R = shape * abs(ER / ET)**2
973	975	return self.scale_simulation(self.convolute_resolution(lai, R))
974	976
975		def densityprofile(self, nz, plot=False):
	977	def densityprofile(self, nz, plot=False, individual_layers=False):
976	978	"""
977	979	calculates the electron density of the layerstack from the thickness
978	980	and roughness of the individual layers

983	985	number of values on which the profile should be calculated
984	986	plot : bool, optional
985	987	flag to tell if a plot of the profile should be created
	988	individual_layers : bool, optional
	989	return the density contributions of all layers as additional return
	990	value.
986	991
987	992	Returns
988	993	-------

990	995	z-coordinates, z = 0 corresponds to the surface
991	996	eprof : array-like
992	997	electron profile
	998	layereprof : 2D array, optional
	999	electron profile of every sublayer with shape (nlayer, nz). This
	1000	is only returned when individual_layers=True
993	1001	"""
994	1002	if plot:
995	1003	try:

1047	1055	sdown = (1 + erf((zdownint - z) / sigint / numpy.sqrt(2))) / 2
1048	1056	w[i, :] = sup - sdown
1049	1057
1050		prof = numpy.sum(dr[:, numpy.newaxis] * w[:, ...], axis=0)
	1058	layer_prof = dr[:, numpy.newaxis] * w[:, ...]
	1059	prof = numpy.sum(layer_prof, axis=0)
1051	1060
1052	1061	if plot:
1053	1062	plt.figure('XU:density_profile', figsize=(5, 3))
	1063	for i, layer in enumerate(self.lstack):
	1064	plt.plot(z, layer_prof[i, :], ':r', lw=1, label=layer.name)
1054	1065	plt.plot(z, prof, '-k', lw=2, label='electron density')
1055	1066	plt.xlabel(r'z ($\mathrm{\AA}$)')
1056	1067	plt.ylabel(r'electron density (e$^-$ cm$^{-3}$)')
1057	1068	plt.tight_layout()
1058	1069
	1070	if individual_layers:
	1071	return z, prof, layer_prof
1059	1072	return z, prof
1060	1073
1061	1074

1343	1356	else:
1344	1357	shape = numpy.ones(np)
1345	1358
1346		ETs = numpy.ones(np, dtype=numpy.complex)
1347		ERs = numpy.zeros(np, dtype=numpy.complex)
	1359	ETs = numpy.ones(np, dtype=complex)
	1360	ERs = numpy.zeros(np, dtype=complex)
1348	1361	ks = -self.exp.k0 * numpy.sqrt(sai*2 - 2 cd[0] * rho[0])
1349	1362
1350	1363	for i in range(ns):

1615	1628	k-vector, z-component of k-vector in the material.
1616	1629	"""
1617	1630	k0 = -K * numpy.sin(alphai)
1618		kz = numpy.zeros((N+1, NqL, Nqz), dtype=numpy.complex)
1619		T = numpy.zeros((N+1, NqL, Nqz), dtype=numpy.complex)
1620		R = numpy.zeros((N+1, NqL, Nqz), dtype=numpy.complex)
	1631	kz = numpy.zeros((N+1, NqL, Nqz), dtype=complex)
	1632	T = numpy.zeros((N+1, NqL, Nqz), dtype=complex)
	1633	R = numpy.zeros((N+1, NqL, Nqz), dtype=complex)
1621	1634	for jn in range(N+1):
1622	1635	kz[jn, ...] = -K * numpy.sqrt(numpy.sin(alphai)**2 -
1623	1636	2 * delta[jn])
1624	1637
1625		T[N, ...] = numpy.ones((NqL, Nqz), dtype=numpy.complex)
	1638	T[N, ...] = numpy.ones((NqL, Nqz), dtype=complex)
1626	1639	kzs = kz[N, ...] # kz in substrate
1627	1640	for jn in range(N-1, -1, -1):
1628	1641	kzn = kz[jn, ...]

1681	1694	psi : array-like
1682	1695	correlation function
1683	1696	"""
1684		psi = numpy.zeros((NqL, Nqz), dtype=numpy.complex)
	1697	psi = numpy.zeros((NqL, Nqz), dtype=complex)
1685	1698	if H == 0.5 or H == 1:
1686		dpsi = numpy.zeros_like(psi, dtype=numpy.complex)
	1699	dpsi = numpy.zeros_like(psi, dtype=complex)
1687	1700	m = isurf > 0
1688	1701	n = 1
1689	1702	s = numpy.copy(b)

1834	1847	T2 = 2 * k02 / (k02 + kz2)
1835	1848	R01 = (k01 - kz1) / (k01 + kz1)
1836	1849	R02 = (k02 - kz2) / (k02+kz2)
1837		R1 = numpy.zeros((NqL, Nqz), dtype=numpy.complex)
	1850	R1 = numpy.zeros((NqL, Nqz), dtype=complex)
1838	1851	R2 = numpy.copy(R1)
1839	1852	nproc = 1
1840	1853	else: # method == 2

1857	1870	z[jn] = z[jn-1] - thick[jn-1]
1858	1871
1859	1872	# calculation of the deltas
1860		delt = numpy.zeros(N+1, dtype=numpy.complex)
	1873	delt = numpy.zeros(N+1, dtype=complex)
1861	1874	for jn in range(N+1):
1862	1875	if jn == 0:
1863	1876	delt[jn] = delta[jn]

+1

-1

lib/xrayutilities/simpack/mosaicity.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2019-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import math
18	18

+21

-21

lib/xrayutilities/simpack/powder.py less more

13	13	# You should have received a copy of the GNU General Public License
14	14	# along with this program; if not, see <http://www.gnu.org/licenses/>.
15	15	#
16		# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
17	16	# Copyright (C) 2015-2017 Marcus H. Mendenhall <marcus.mendenhall@nist.gov>
	17	# Copyright (C) 2017-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
18	18
19	19	# FP_profile was derived from http://dx.doi.org/10.6028/jres.120.014.c
20	20

137	137	]
138	138
139	139	ft_factors.sort()
140		ft_factors = numpy.array(ft_factors, numpy.int)
	140	ft_factors = numpy.array(ft_factors, int)
141	141
142	142	# used for debugging moments from FP_profile.axial_helper().
143	143	moment_list = []

350	350	b = self.add_buffer # shortcut
351	351
352	352	# a real-format scratch buffer
353		self._rb1 = b(numpy.zeros(nn, numpy.float))
	353	self._rb1 = b(numpy.zeros(nn, float))
354	354	# a real-format scratch buffer
355		self._rb2 = b(numpy.zeros(nn, numpy.float))
	355	self._rb2 = b(numpy.zeros(nn, float))
356	356	# a real-format scratch buffer
357		self._rb3 = b(numpy.zeros(nn, numpy.float))
	357	self._rb3 = b(numpy.zeros(nn, float))
358	358	# a complex-format scratch buffer
359		self._cb1 = b(numpy.zeros(nn, numpy.complex))
	359	self._cb1 = b(numpy.zeros(nn, complex))
360	360	# a scratch buffer used by the axial helper
361	361	self._f0buf = b(numpy.zeros(self.oversampling *
362		twotheta_output_points, numpy.float))
	362	twotheta_output_points, float))
363	363	# a scratch buffer used for axial divergence
364	364	self._epsb2 = b(numpy.zeros(self.oversampling *
365		twotheta_output_points, numpy.float))
	365	twotheta_output_points, float))
366	366	# the I2+ buffer
367	367	self._I2p = b(numpy.zeros(self.oversampling *
368		twotheta_output_points, numpy.float))
	368	twotheta_output_points, float))
369	369	# the I2- buffer
370	370	self._I2m = b(numpy.zeros(self.oversampling *
371		twotheta_output_points, numpy.float))
	371	twotheta_output_points, float))
372	372	# another buffer used for axial divergence
373	373	self._axial = b(numpy.zeros(self.oversampling *
374		twotheta_output_points, numpy.float))
	374	twotheta_output_points, float))
375	375	# the largest frequency in Fourier space
376	376	omega_max = self.n_omega_points * 2 * pi / window_fullwidth
377	377	# build the x grid and the complex array that is the convolver

460	460	"""
461	461	self.param_dicts["conv_" + convolver].update(kwargs)
462	462
463		def get_conv(self, name, key, format=numpy.float):
	463	def get_conv(self, name, key, format=float):
464	464	"""
465	465	get a cached, pre-computed convolver associated with the given
466	466	parameters, or a newly zeroed convolver if the cache doesn't contain

1043	1043	if "equatorial_divergence_deg" in kwargs:
1044	1044	del kwargs["equatorial_divergence_deg"] # not used
1045	1045
1046		flag, axfn = self.get_conv(me, kwargs, numpy.complex)
	1046	flag, axfn = self.get_conv(me, kwargs, complex)
1047	1047	if flag:
1048	1048	return axfn # already up to date if first return is True
1049	1049

1085	1085	# we also need the diffractometer radius from the global space
1086	1086	kwargs["diffractometer_radius"] = self.param_dicts[
1087	1087	"conv_global"]["diffractometer_radius"]
1088		flag, tailfn = self.get_conv(me, kwargs, numpy.complex)
	1088	flag, tailfn = self.get_conv(me, kwargs, complex)
1089	1089	if flag:
1090	1090	return tailfn # already up to date
1091	1091

1145	1145	"""
1146	1146	if width is None:
1147	1147	return # no convolver
1148		flag, conv = self.get_conv(name, width, numpy.float)
	1148	flag, conv = self.get_conv(name, width, float)
1149	1149	if flag:
1150	1150	return conv # already up to date
1151	1151	rb1 = self._rb1

1240	1240	if hasattr(v, 'tolist'):
1241	1241	key[k] = v.tolist()
1242	1242
1243		flag, emiss = self.get_conv(me, key, numpy.complex)
	1243	flag, emiss = self.get_conv(me, key, complex)
1244	1244	if flag:
1245	1245	return emiss # already up to date
1246	1246

1302	1302	return None
1303	1303	twotheta0 = self.param_dicts["conv_global"]["twotheta0"]
1304	1304	key = (twotheta0, equatorial_divergence_deg)
1305		flag, conv = self.get_conv(me, key, numpy.complex)
	1305	flag, conv = self.get_conv(me, key, complex)
1306	1306	if flag:
1307	1307	return conv # already up to date
1308	1308

1343	1343	kwargs["diffractometer_radius"] = self.param_dicts[
1344	1344	"conv_global"]["diffractometer_radius"]
1345	1345
1346		flag, conv = self.get_conv(me, kwargs, numpy.complex)
	1346	flag, conv = self.get_conv(me, kwargs, complex)
1347	1347	if flag:
1348	1348	return conv # already up to date
1349	1349	xx = type("data", (), kwargs) # make it dot-notation accessible

1396	1396	flag, conv = self.get_conv(me,
1397	1397	(twotheta0, diffractometer_radius,
1398	1398	specimen_displacement, zero_error_deg),
1399		numpy.complex)
	1399	complex)
1400	1400	if flag:
1401	1401	return conv # already up to date
1402	1402

1455	1455	return None
1456	1456	kwargs.update(self.param_dicts["conv_global"])
1457	1457
1458		flag, conv = self.get_conv(me, kwargs, numpy.float)
	1458	flag, conv = self.get_conv(me, kwargs, float)
1459	1459	if flag:
1460	1460	return conv # already up to date
1461	1461

1506	1506	if not self.gaussian_smoother_bins_sigma:
1507	1507	return # no smoothing
1508	1508	flag, buf = self.get_conv(me, self.gaussian_smoother_bins_sigma,
1509		format=numpy.float)
	1509	format=float)
1510	1510	if flag:
1511	1511	return buf # already computed
1512	1512	buf[:] = self.omega_vals

+2

-2

lib/xrayutilities/simpack/powdermodel.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016-2017 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2017-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import numbers
18	18	from math import sqrt

573	573	if exp is not None:
574	574	ax.plot(twotheta, exp, formatexp, label=labelexp)
575	575	if mask is None:
576		mask = numpy.ones_like(twotheta, dtype=numpy.bool)
	576	mask = numpy.ones_like(twotheta, dtype=bool)
577	577	if isinstance(sim, PowderModel):
578	578	simdata = sim.simulate(twotheta[mask])
579	579	sim.plot(twotheta[mask], label=labelsim, formatspec=formatsim, ax=ax)

+1

-1

lib/xrayutilities/simpack/smaterials.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import collections.abc
18	18	import copy

+1

-1

lib/xrayutilities/utilities_noconf.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2010-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2010-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	"""
18	18	xrayutilities utilities contains a conglomeration of useful functions

+2

-2

lib/xrayutilities.egg-info/PKG-INFO less more

11	11	=============
12	12
13	13
14		[![Build Status](https://dev.azure.com/dominikkriegner/xrayutilities/_apis/build/status/dkriegner.xrayutilities?repoName=dkriegner%2Fxrayutilities&branchName=master)](https://dev.azure.com/dominikkriegner/xrayutilities/_build/latest?definitionId=1&repoName=dkriegner%2Fxrayutilities&branchName=master)
	14	[![Build Status](https://dev.azure.com/dominikkriegner/xrayutilities/_apis/build/status/dkriegner.xrayutilities?repoName=dkriegner%2Fxrayutilities&branchName=main)](https://dev.azure.com/dominikkriegner/xrayutilities/_build/)
15	15
16	16	xrayutilities is a collection of scripts used to analyze and simulate x-ray
17	17	diffraction data. It consists of a Python package and several routines coded

215	215	Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
216	216	Requires-Python: ~=3.6
217	217	Description-Content-Type: text/markdown
	218	Provides-Extra: fit
218	219	Provides-Extra: plot
219		Provides-Extra: fit

+1

-1

lib/xrayutilities.egg-info/SOURCES.txt less more

1	1	LICENSE.txt
2	2	MANIFEST.in
3	3	README.md
	4	pyproject.toml
4	5	setup.py
5	6	doc/source/conf.py
6	7	doc/source/example_xu_ccd_parameter.py

171	172	src/qconversion.c
172	173	src/qconversion.h
173	174	src/xrayutilities.h
174		tests/__init__.py
175	175	tests/test_HXRD.py
176	176	tests/test_NonCOP.py
177	177	tests/test_alloy_content_calc.py

+1

-1

lib/xrayutilities.egg-info/requires.txt less more

	0	h5py
0	1	numpy>=1.9.2
1	2	scipy>=0.13.0
2		h5py
3	3
4	4	[fit]
5	5	lmfit>=1.0.1

+47

-0

pyproject.toml less more

	0	[build-system]
	1	requires = ["setuptools", "wheel", "numpy"]
	2	build-backend = "setuptools.build_meta"
	3
	4	[tool.coverage.paths]
	5	source = [
	6	"lib",
	7	"*/site-packages"
	8	]
	9
	10	[tool.coverage.run]
	11	branch = true
	12	parallel = true
	13	source = [
	14	"xrayutilities"
	15	]
	16
	17	[tool.tox]
	18	legacy_tox_ini = """
	19	[tox]
	20	envlist = py{36,37,38,39},coverage
	21	distshare = {toxinidir}/dist
	22
	23	[testenv]
	24	wheel = true
	25	allowlist_externals =
	26	mv
	27	deps =
	28	h5py
	29	lmfit
	30	matplotlib
	31	numpy
	32	scipy
	33	pytest
	34	pytest-cov
	35	coverage[toml]
	36	commands =
	37	pytest --cov --cov-config pyproject.toml --junitxml=.tox/junit.{envname}.xml --cov-report=xml:.tox/coverage.xml
	38	mv .coverage .tox/.coverage.{envname}
	39
	40	[testenv:coverage]
	41	commands =
	42	coverage combine .tox/
	43	coverage xml -i -o .tox/coverage.xml
	44	coverage report -i
	45	mv .coverage .tox/
	46	"""

+4

-4

setup.py less more

184	184	"Development Status :: 5 - Production/Stable",
185	185	"License :: OSI Approved :: GNU General Public License v2 or later "
186	186	"(GPLv2+)"
187		],
	187	],
188	188	long_description=long_description,
189	189	long_description_content_type="text/markdown",
190	190	author_email="eugen.wintersberger@desy.de, dominik.kriegner@gmail.com",

195	195	package_data={
196	196	"xrayutilities": ["VERSION", "*.conf"],
197	197	"xrayutilities.materials": [os.path.join("data", "*")]
198		},
	198	},
199	199	python_requires='~=3.6',
200	200	setup_requires=['numpy', 'scipy', 'h5py'],
201	201	install_requires=['numpy>=1.9.2', 'scipy>=0.13.0', 'h5py'],
202	202	extras_require={
203	203	'plot': ["matplotlib>=3.1.0"],
204	204	'fit': ["lmfit>=1.0.1"],
205		},
	205	},
206	206	include_dirs=[numpy.get_include()],
207	207	ext_modules=[extmodul],
208	208	cmdclass=cmdclass,
209	209	url="https://xrayutilities.sourceforge.io",
210	210	license="GPLv2",
211	211	script_args=args
212		)
	212	)

+2

-2

src/qconversion.c less more

13	13	* You should have received a copy of the GNU General Public License
14	14	* along with this program; if not, see <http://www.gnu.org/licenses/>.
15	15	*
16		* Copyright (C) 2010-2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	* Copyright (C) 2010-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17	*/
18	18
19	19	/* ######################################

131	131	}
132	132	}
133	133
134		INLINE void tensorprod(double RESTRICT v1, double RESTRICT v2,
	134	INLINE void tensorprod(double v1, double v2,
135	135	double *RESTRICT m) {
136	136	unsigned int i, j;
137	137	for (i = 0; i < 3; i = i + 1) {

+2

-2

src/qconversion.h less more

13	13	* You should have received a copy of the GNU General Public License
14	14	* along with this program; if not, see <http://www.gnu.org/licenses/>.
15	15	*
16		* Copyright (C) 2013-2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	* Copyright (C) 2013-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
17	17	*/
18	18	#pragma once
19	19

63	63	INLINE void matvec(double RESTRICT m, double RESTRICT v,
64	64	double *RESTRICT r);
65	65
66		INLINE void tensorprod(double RESTRICT v1, double RESTRICT v2,
	66	INLINE void tensorprod(double v1, double v2,
67	67	double *RESTRICT m);
68	68
69	69	INLINE void summat(double RESTRICT m1, double RESTRICT m2);

+0

-17

~~tests/__init__.py~~ less more

0		# This file is part of xrayutilities.
1		#
2		# xrayutilities is free software; you can redistribute it and/or modify
3		# it under the terms of the GNU General Public License as published by
4		# the Free Software Foundation; either version 2 of the License, or
5		# (at your option) any later version.
6		#
7		# This program is distributed in the hope that it will be useful,
8		# but WITHOUT ANY WARRANTY; without even the implied warranty of
9		# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10		# GNU General Public License for more details.
11		#
12		# You should have received a copy of the GNU General Public License
13		# along with this program; if not, see <http://www.gnu.org/licenses/>.
14		#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
16		# 2016 Eugen Wintersberger <eugen.wintersberger@desy.de>

+1

-1

tests/test_HXRD.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_NonCOP.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_alloy_content_calc.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_amorphous.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2016 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_analysis_linecuts.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2018 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2018-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import math
18	18	import unittest

+1

-1

tests/test_blockaverage.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_ccd_normalizer.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_examples.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2019-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os
18	18	import subprocess

+1

-1

tests/test_fuzzygridder1d.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_fuzzygridder2d.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_fuzzygridder3d.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_getang.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014-2018 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_gridder1d.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_gridder2d.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_gridder2dlist.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_gridder3d.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_io_esg.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_fastscan.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_nja.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_nja_map.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_nja_tsk.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_numor.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_pdcif.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_perkinelmer.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_pilatus.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_rigaku.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_roperccd.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2017 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_spec.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015,2018 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import tempfile

+1

-1

tests/test_io_specalignmentlog.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_speclog.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_specsardana.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2019-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import math
18	18	import os.path

+1

-1

tests/test_io_tty.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_io_xrdml.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015-2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_linear_calib.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_maplog.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_materials.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2017-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import math
18	18	import unittest

+1

-1

tests/test_materials_cif.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2017 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os.path
18	18	import unittest

+1

-1

tests/test_materials_cifexport.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2018-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os
18	18	import tempfile

+1

-1

tests/test_materials_database.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import math
18	18	import os

+1

-1

tests/test_materials_findsym.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_math_peak_fit.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_math_solve_quartic.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_math_vector.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2012-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_miscut_calc.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_npygridder1d.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_optical_properties.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_pseudomorphic.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2016-2017 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2016-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import math
18	18	import unittest

+1

-1

tests/test_q2angfit.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_qconversion.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014-2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_qconversion_area.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014-2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_qconversion_linear.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014-2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2013-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_qconversion_trans.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2014 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2014-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_simpack_dynamicalmodel.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2019-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+3

-1

tests/test_simpack_kinematicalmodel.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2019-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
	16	#
	17
16	18
17	19	import unittest
18	20

+2

-2

tests/test_simpack_powdermodel.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2017 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2017-2021 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import os
18	18	import unittest

139	139
140	140
141	141	if __name__ == '__main__':
142		freeze_support()
	142	freeze_support() # required for MS Windows
143	143	unittest.main()

+1

-1

tests/test_simpack_xrrdiffuse.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2018 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2018-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_simpack_xrrspecular.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2019 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2019-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_structure_factor.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18

+1

-1

tests/test_transforms.py less more

12	12	# You should have received a copy of the GNU General Public License
13	13	# along with this program; if not, see <http://www.gnu.org/licenses/>.
14	14	#
15		# Copyright (C) 2015 Dominik Kriegner <dominik.kriegner@gmail.com>
	15	# Copyright (C) 2015-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
16	16
17	17	import unittest
18	18