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1	# -- coding: utf-8 --
2	#GSASIIobj - data objects for GSAS-II
3	########### SVN repository information ###################
4	# $Date: 2021-12-06 22:56:47 +0000 (Mon, 06 Dec 2021) $
5	# $Author: toby $
6	# $Revision: 5110 $
7	# $URL: trunk/GSASIIobj.py $
8	# $Id: GSASIIobj.py 5110 2021-12-06 22:56:47Z toby $
9	########### SVN repository information ###################
10
11	'''
12	GSASIIobj: Data objects
13	=========================
14
15	This module defines and/or documents the data structures used in GSAS-II, as well
16	as provides misc. support routines.
17
18	.. Next command allows \\AA to be used in HTML
19
20	.. only:: html
21
22	:math:`\\require{mediawiki-texvc}`
23
24	.. _Constraints_table:
25
26	.. index::
27	single: Constraints object description
28	single: Data object descriptions; Constraints
29
30	Constraints Tree Item
31	----------------------
32
33	Constraints are stored in a dict, separated into groups.
34	Note that parameter are named in the following pattern,
35	p:h:<var>:n, where p is the phase number, h is the histogram number
36	<var> is a variable name and n is the parameter number.
37	If a parameter does not depend on a histogram or phase or is unnumbered, that
38	number is omitted.
39	Note that the contents of each dict item is a List where each element in the
40	list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
41	The constraints in this form are converted in
42	:func:`GSASIImapvars.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
43
44	The keys in the Constraints dict are:
45
46	.. tabularcolumns:: \|l\|p{4.5in}\|
47
48	========== ====================================================
49	key explanation
50	========== ====================================================
51	Hist This specifies a list of constraints on
52	histogram-related parameters,
53	which will be of form :h:<var>:n.
54	HAP This specifies a list of constraints on parameters
55	that are defined for every histogram in each phase
56	and are of form p:h:<var>:n.
57	Phase This specifies a list of constraints on phase
58	parameters,
59	which will be of form p::<var>:n.
60	Global This specifies a list of constraints on parameters
61	that are not tied to a histogram or phase and
62	are of form ::<var>:n
63	========== ====================================================
64
65	.. _Constraint_definitions_table:
66
67	.. index::
68	single: Constraint definition object description
69	single: Data object descriptions; Constraint Definition
70
71	Each constraint is defined as an item in a list. Each constraint is of form::
72
73	[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
74
75	Where the variable pair list item containing two values [<mult>, <var>], where:
76
77	* <mult> is a multiplier for the constraint (float)
78	* <var> a :class:`G2VarObj` object. (Note that in very old .gpx files this might be a str with a variable name of form 'p:h:name[:at]')
79
80	Note that the last three items in the list play a special role:
81
82	* <fixedval> is the fixed value for a `constant equation` (``constype=c``)
83	constraint or is None. For a `New variable` (``constype=f``) constraint,
84	a variable name can be specified as a str (used for externally
85	generated constraints)
86	* <varyflag> is True or False for `New variable` (``constype=f``) constraints
87	or is None. This indicates if this variable should be refined.
88	* <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
89
90	* 'e' defines a set of equivalent variables. Only the first variable is refined (if the
91	appropriate refine flag is set) and and all other equivalent variables in the list
92	are generated from that variable, using the appropriate multipliers.
93	* 'c' defines a constraint equation of form,
94	:math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
95	* 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
96	even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
97	constraint and the mult value is ignored.
98	This is of particular value when needing to hold one or more variables where a
99	single flag controls a set of variables such as, coordinates,
100	the reciprocal metric tensor or anisotropic displacement parameter.
101	* 'f' defines a new variable (function) according to relationship
102	:math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
103
104	.. _Covariance_table:
105
106	.. index::
107	single: Covariance description
108	single: Data object descriptions; Covariance
109
110	Covariance Tree Item
111	--------------------
112
113	The Covariance tree item has results from the last least-squares run. They
114	are stored in a dict with these keys:
115
116	.. tabularcolumns:: \|l\|l\|p{4in}\|
117
118	============= =============== ====================================================
119	key sub-key explanation
120	============= =============== ====================================================
121	newCellDict \\ (dict) ith lattice parameters computed by
122	:func:`GSASIIstrMath.GetNewCellParms`
123	title \\ (str) Name of gpx file(?)
124	variables \\ (list) Values for all N refined variables
125	(list of float values, length N,
126	ordered to match varyList)
127	sig \\ (list) Uncertainty values for all N refined variables
128	(list of float values, length N,
129	ordered to match varyList)
130	varyList \\ (list of str values, length N) List of directly refined variables
131
132	newAtomDict \\ (dict) atom position values computed in
133	:func:`GSASIIstrMath.ApplyXYZshifts`
134	Rvals \\ (dict) R-factors, GOF, Marquardt value for last
135	refinement cycle
136	\\ Nobs (int) Number of observed data points
137	\\ Rwp (float) overall weighted profile R-factor (%)
138	\\ chisq (float) :math:`\\sum w*(I_{obs}-I_{calc})^2`
139	for all data.
140	Note: this is not the reduced :math:`\\chi^2`.
141	\\ lamMax (float) Marquardt value applied to Hessian diagonal
142	\\ GOF (float) The goodness-of-fit, aka square root of
143	the reduced chi squared.
144	covMatrix \\ (np.array) The (NxN) covVariance matrix
145	============= =============== ====================================================
146
147	.. _Phase_table:
148
149	.. index::
150	single: Phase object description
151	single: Data object descriptions; Phase
152
153	Phase Tree Items
154	----------------
155
156	Phase information is stored in the GSAS-II data tree as children of the
157	Phases item in a dict with keys:
158
159	.. tabularcolumns:: \|l\|l\|p{4in}\|
160
161	========== =============== =====================================================================================================
162	key sub-key explanation
163	========== =============== =====================================================================================================
164	General \\ (dict) Overall information for the phase
165	\\ 3Dproj (list of str) projections for 3D pole distribution plots
166	\\ AngleRadii (list of floats) Default radius for each atom used to compute
167	interatomic angles
168	\\ AtomMass (list of floats) Masses for atoms
169	\\ AtomPtrs (list of int) four locations (cx,ct,cs & cu) to use to pull info
170	from the atom records
171	\\ AtomTypes (llist of str) Atom types
172	\\ BondRadii (list of floats) Default radius for each atom used to compute
173	interatomic distances
174	\\ Cell Unit cell parameters & ref. flag
175	(list with 8 items. All but first item are float.)
176
177	0: cell refinement flag (True/False),
178	1-3: a, b, c, (:math:`\\AA`)
179	4-6: alpha, beta & gamma, (degrees)
180	7: volume (:math:`\\AA^3`)
181	\\ Color (list of (r,b,g) triplets) Colors for atoms
182	\\ Compare (dict) Polygon comparison parameters
183	\\ Data plot type (str) data plot type ('Mustrain', 'Size' or
184	'Preferred orientation') for powder data
185	\\ DisAglCtls (dDict) with distance/angle search controls,
186	which has keys 'Name', 'AtomTypes',
187	'BondRadii', 'AngleRadii' which are as above
188	except are possibly edited. Also contains
189	'Factors', which is a 2 element list with
190	a multiplier for bond and angle search range
191	[typically (0.85,0.85)].
192	\\ F000X (float) x-ray F(000) intensity
193	\\ F000N (float) neutron F(000) intensity
194	\\ Flip (dict) Charge flip controls
195	\\ HydIds (dict) geometrically generated hydrogen atoms
196	\\ Isotope (dict) Isotopes for each atom type
197	\\ Isotopes (dict) Scattering lengths for each isotope
198	combination for each element in phase
199	\\ MCSA controls (dict) Monte Carlo-Simulated Annealing controls
200	\\ Map (dict) Map parameters
201	\\ Mass (float) Mass of unit cell contents in g/mol
202	\\ Modulated (bool) True if phase modulated
203	\\ Mydir (str) Directory of current .gpx file
204	\\ Name (str) Phase name
205	\\ NoAtoms (dict) Number of atoms per unit cell of each type
206	\\ POhkl (list) March-Dollase preferred orientation direction
207	\\ Pawley dmin (float) maximum Q (as d-space) to use for Pawley extraction
208	\\ Pawley dmax (float) minimum Q (as d-space) to use for Pawley extraction
209	\\ Pawley neg wt (float) Restraint value for negative Pawley intensities
210	\\ SGData (object) Space group details as a
211	:ref:`space group (SGData) <SGData_table>`
212	object, as defined in :func:`GSASIIspc.SpcGroup`.
213	\\ SH Texture (dict) Spherical harmonic preferred orientation parameters
214	\\ Super (int) dimension of super group (0,1 only)
215	\\ Type (str) phase type (e.g. 'nuclear')
216	\\ Z (dict) Atomic numbers for each atom type
217	\\ doDysnomia (bool) flag for max ent map modification via Dysnomia
218	\\ doPawley (bool) Flag for Pawley intensity extraction
219	\\ vdWRadii (dict) Van der Waals radii for each atom type
220	ranId \\ (int) unique random number Id for phase
221	pId \\ (int) Phase Id number for current project.
222	Atoms \\ (list of lists) Atoms in phase as a list of lists. The outer list
223	is for each atom, the inner list contains varying
224	items depending on the type of phase, see
225	the :ref:`Atom Records <Atoms_table>` description.
226	Drawing \\ (dict) Display parameters
227	\\ Atoms (list of lists) with an entry for each atom that is drawn
228	\\ Plane (list) Controls for contour density plane display
229	\\ Quaternion (4 element np.array) Viewing quaternion
230	\\ Zclip (float) clipping distance in :math:`\\AA`
231	\\ Zstep (float) Step to de/increase Z-clip
232	\\ atomPtrs (list) positions of x, type, site sym, ADP flag in Draw Atoms
233	\\ backColor (list) background for plot as and R,G,B triplet
234	(default = [0, 0, 0], black).
235	\\ ballScale (float) Radius of spheres in ball-and-stick display
236	\\ bondList (dict) Bonds
237	\\ bondRadius (float) Radius of binds in :math:`\\AA`
238	\\ cameraPos (float) Viewing position in :math:`\\AA` for plot
239	\\ contourLevel (float) map contour level in :math:`e/\\AA^3`
240	\\ contourMax (float) map contour maximum
241	\\ depthFog (bool) True if use depthFog on plot - set currently as False
242	\\ ellipseProb (float) Probability limit for display of thermal
243	ellipsoids in % .
244	\\ magMult (float) multiplier for magnetic moment arrows
245	\\ mapSize (float) x & y dimensions of contourmap (fixed internally)
246	\\ modelView (4,4 array) from openGL drawing transofmation matrix
247	\\ oldxy (list with two floats) previous view point
248	\\ radiusFactor (float) Distance ratio for searching for bonds. Bonds
249	are located that are within r(Ra+Rb) and (Ra+Rb)/r
250	where Ra and Rb are the atomic radii.
251	\\ selectedAtoms (list of int values) List of selected atoms
252	\\ showABC (bool) Flag to show view point triplet. True=show.
253	\\ showHydrogen (bool) Flag to control plotting of H atoms.
254	\\ showRigidBodies (bool) Flag to highlight rigid body placement
255	\\ showSlice (bool) flag to show contour map
256	\\ sizeH (float) Size ratio for H atoms
257	\\ unitCellBox (bool) Flag to control display of the unit cell.
258	\\ vdwScale (float) Multiplier of van der Waals radius for display of vdW spheres.
259	\\ viewDir (np.array with three floats) cartesian viewing direction
260	\\ viewPoint (list of lists) First item in list is [x,y,z]
261	in fractional coordinates for the center of
262	the plot. Second item list of previous & current
263	atom number viewed (may be [0,0])
264	RBModels \\ Rigid body assignments (note Rigid body definitions
265	are stored in their own main top-level tree entry.)
266	RMC \\ (dict) RMCProfile & rmcfull controls
267	Pawley ref \\ (list) Pawley reflections
268	Histograms \\ (dict of dicts) The key for the outer dict is
269	the histograms tied to this phase. The inner
270	dict contains the combined phase/histogram
271	parameters for items such as scale factors,
272	size and strain parameters. The following are the
273	keys to the inner dict. (dict)
274	\\ Babinet (dict) For protein crystallography. Dictionary with two
275	entries, 'BabA', 'BabU'
276	\\ Extinction (list of float, bool) Extinction parameter
277	\\ Flack (list of [float, bool]) Flack parameter & refine flag
278	\\ HStrain (list of two lists) Hydrostatic strain. The first is
279	a list of the HStrain parameters (1, 2, 3, 4, or 6
280	depending on unit cell), the second is a list of boolean
281	refinement parameters (same length)
282	\\ Histogram (str) The name of the associated histogram
283	\\ Layer Disp (list of [float, bool]) Layer displacement in beam direction & refine flag
284	\\ LeBail (bool) Flag for LeBail extraction
285	\\ Mustrain (list) Microstrain parameters, in order:
286
287	0. Type, one of u'isotropic', u'uniaxial', u'generalized'
288	1. Isotropic/uniaxial parameters - list of 3 floats
289	2. Refinement flags - list of 3 bools
290	3. Microstrain axis - list of 3 ints, [h, k, l]
291	4. Generalized mustrain parameters - list of 2-6 floats, depending on space group
292	5. Generalized refinement flags - list of bools, corresponding to the parameters of (4)
293	\\ Pref.Ori. (list) Preferred Orientation. List of eight parameters.
294	Items marked SH are only used for Spherical Harmonics.
295
296	0. (str) Type, 'MD' for March-Dollase or 'SH' for Spherical Harmonics
297	1. (float) Value
298	2. (bool) Refinement flag
299	3. (list) Preferred direction, list of ints, [h, k, l]
300	4. (int) SH - number of terms
301	5. (dict) SH -
302	6. (list) SH
303	7. (float) SH
304	\\ Scale (list of [float, bool]) Phase fraction & refine flag
305	\\ Size List of crystallite size parameters, in order:
306
307	0. (str) Type, one of u'isotropic', u'uniaxial', u'ellipsoidal'
308	1. (list) Isotropic/uniaxial parameters - list of 3 floats
309	2. (list) Refinement flags - list of 3 bools
310	3. (list) Size axis - list of 3 ints, [h, k, l]
311	4. (list) Ellipsoidal size parameters - list of 6 floats
312	5. (list) Ellipsoidal refinement flags - list of bools, corresponding to the parameters of (4)
313	\\ Use (bool) True if this histogram is to be used in refinement
314	MCSA \\ (dict) Monte-Carlo simulated annealing parameters
315	========== =============== =====================================================================================================
316
317	.. _RBData_table:
318
319	.. index::
320	single: Rigid Body Data description
321	single: Data object descriptions; Rigid Body Data
322
323	Rigid Body Objects
324	------------------
325
326	Rigid body descriptions are available for two types of rigid bodies: 'Vector'
327	and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
328	with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
329	with defined refinable torsion angles.
330
331	.. tabularcolumns:: \|l\|l\|p{4in}\|
332
333	========== =============== ====================================================
334	key sub-key explanation
335	========== =============== ====================================================
336	Vector RBId (dict of dict) vector rigid bodies
337	\\ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type
338	\\ RBname (str) Name assigned by user to rigid body
339	\\ VectMag (list) vector magnitudes in :math:`\\AA`
340	\\ rbXYZ (list of 3 float Cartesian coordinates for Vector rigid body )
341	\\ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
342	definition, use center of atoms flag
343	\\ VectRef (list of bool refinement flags for VectMag values )
344	\\ rbTypes (list of str) Atom types for each atom in rigid body
345	\\ rbVect (list of lists) Cartesian vectors for each translation used to build rigid body
346	\\ useCount (int) Number of times rigid body is used in any structure
347	Residue RBId (dict of dict) residue rigid bodies
348	\\ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type
349	\\ RBname (str) Name assigned by user to rigid body
350	\\ rbXYZ (list of 3 float) Cartesian coordinates for Residue rigid body
351	\\ rbTypes (list of str) Atom types for each atom in rigid body
352	\\ atNames (list of str) Names of each atom in rigid body (e.g. C1,N2...)
353	\\ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
354	definition, use center of atoms flag
355	\\ rbSeq (list) Orig,Piv,angle,Riding : definition of internal rigid body
356	torsion; origin atom (int), pivot atom (int), torsion angle (float),
357	riding atoms (list of int)
358	\\ SelSeq (int,int) used by SeqSizer to identify objects
359	\\ useCount (int)Number of times rigid body is used in any structure
360	RBIds \\ (dict) unique Ids generated upon creation of each rigid body
361	\\ Vector (list) Ids for each Vector rigid body
362	\\ Residue (list) Ids for each Residue rigid body
363	========== =============== ====================================================
364
365	.. _SGData_table:
366
367	.. index::
368	single: Space Group Data description
369	single: Data object descriptions; Space Group Data
370
371	Space Group Objects
372	-------------------
373
374	Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
375	and the information is placed in a SGdata object
376	which is a dict with these keys. Magnetic ones are marked "mag"
377
378	.. tabularcolumns:: \|l\|p{4.5in}\|
379
380	========== ========================================================================================
381	key explanation
382	========== ========================================================================================
383	BNSlattsym mag - (str) BNS magnetic space group symbol and centering vector
384	GenFlg mag - (list) symmetry generators indices
385	GenSym mag - (list) names for each generator
386	MagMom mag - (list) "time reversals" for each magnetic operator
387	MagPtGp mag - (str) Magnetic point group symbol
388	MagSpGrp mag - (str) Magnetic space group symbol
389	OprNames mag - (list) names for each space group operation
390	SGCen (np.array) Symmetry cell centering vectors. A (n,3) np.array
391	of centers. Will always have at least one row: ``np.array([[0, 0, 0]])``
392	SGFixed (bool) Only True if phase mported from a magnetic cif file
393	then the space group can not be changed by the user because
394	operator set from cif may be nonstandard
395	SGGen (list) generators
396	SGGray (bool) True if space group is a gray group (incommensurate magnetic structures)
397	SGInv (bool) True if centrosymmetric, False if not
398	SGLatt (str)Lattice centering type. Will be one of
399	P, A, B, C, I, F, R
400	SGLaue (str) one of the following 14 Laue classes:
401	-1, 2/m, mmm, 4/m, 4/mmm, 3R,
402	3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m
403	SGOps (list) symmetry operations as a list of form
404	``[[M1,T1], [M2,T2],...]``
405	where :math:`M_n` is a 3x3 np.array
406	and :math:`T_n` is a length 3 np.array.
407	Atom coordinates are transformed where the
408	Asymmetric unit coordinates [X is (x,y,z)]
409	are transformed using
410	:math:`X^\\prime = M_n*X+T_n`
411	SGPolax (str) Axes for space group polarity. Will be one of
412	'', 'x', 'y', 'x y', 'z', 'x z', 'y z',
413	'xyz'. In the case where axes are arbitrary
414	'111' is used (P 1, and ?).
415	SGPtGrp (str) Point group of the space group
416	SGUniq unique axis if monoclinic. Will be
417	a, b, or c for monoclinic space groups.
418	Will be blank for non-monoclinic.
419	SGSpin mag - (list) of spin flip operatiors (+1 or -1) for the space group operations
420	SGSys (str) symmetry unit cell: type one of
421	'triclinic', 'monoclinic', 'orthorhombic',
422	'tetragonal', 'rhombohedral', 'trigonal',
423	'hexagonal', 'cubic'
424	SSGK1 (list) Superspace multipliers
425	SpGrp (str) space group symbol
426	SpnFlp mag - (list) Magnetic spin flips for every magnetic space group operator
427	========== ========================================================================================
428
429	.. _SSGData_table:
430
431	.. index::
432	single: Superspace Group Data description
433	single: Data object descriptions; Superspace Group Data
434
435	Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
436	and the information is placed in a SSGdata object
437	which is a dict with these keys:
438
439	.. tabularcolumns:: \|l\|p{4.5in}\|
440
441	========== ====================================================
442	key explanation
443	========== ====================================================
444	SSGCen (list) 4D cell centering vectors [0,0,0,0] at least
445	SSGK1 (list) Superspace multipliers
446	SSGOps (list) 4D symmetry operations as [M,T] so that M*x+T = x'
447	SSpGrp (str) superspace group symbol extension to space group
448	symbol, accidental spaces removed
449	modQ (list) modulation/propagation vector
450	modSymb (list of str) Modulation symbols
451	========== ====================================================
452
453
454	Phase Information
455	--------------------
456
457	.. index::
458	single: Phase information record description
459
460	Phase information is placed in one of the following keys:
461
462	.. tabularcolumns:: \|l\|p{4.5in}\|
463
464	========== ==============================================================
465	key explanation
466	========== ==============================================================
467	General Overall information about a phase
468	Histograms Information about each histogram linked to the
469	current phase as well as parameters that
470	are defined for each histogram and phase
471	(such as sample peak widths and preferred
472	orientation parameters.
473	Atoms Contains a list of atoms, as described in the
474	:ref:`Atom Records <Atoms_table>` description.
475	Drawing Parameters that determine how the phase is
476	displayed, including a list of atoms to be
477	included, as described in the
478	:ref:`Drawing Atom Records <Drawing_atoms_table>`
479	description
480	MCSA Monte-Carlo simulated annealing parameters
481	pId The index of each phase in the project, numbered
482	starting at 0
483	ranId An int value with a unique value for each phase
484	RBModels A list of dicts with parameters for each
485	rigid body inserted into the current phase,
486	as defined in the
487	:ref:`Rigid Body Insertions <Rigid_Body_Insertions>`.
488	Note that the rigid bodies are defined as
489	:ref:`Rigid Body Objects <RBData_table>`
490	RMC PDF modeling parameters
491	Pawley ref Pawley refinement parameters
492
493	========== ==============================================================
494
495	.. _Atoms_table:
496
497	.. index::
498	single: Atoms record description
499	single: Data object descriptions; Atoms record
500
501	--------------------
502	Atom Records
503	--------------------
504
505	If ``phasedict`` points to the phase information in the data tree, then
506	atoms are contained in a list of atom records (list) in
507	``phasedict['Atoms']``. Also needed to read atom information
508	are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
509	which define locations in the atom record, as shown below. Items shown are
510	always present; additional ones for macromolecular phases are marked 'mm',
511	and those for magnetic structures are marked 'mg'
512
513	.. tabularcolumns:: \|l\|p{4.5in}\|
514
515	============== ====================================================
516	location explanation
517	============== ====================================================
518	ct-4 mm - (str) residue number
519	ct-3 mm - (str) residue name (e.g. ALA)
520	ct-2 mm - (str) chain label
521	ct-1 (str) atom label
522	ct (str) atom type
523	ct+1 (str) refinement flags; combination of 'F', 'X', 'U', 'M'
524	cx,cx+1,cx+2 (3 floats) the x,y and z coordinates
525	cx+3 (float) site occupancy
526	cx+4,cx+5,cx+6 mg - (list) atom magnetic moment along a,b,c in Bohr magnetons
527	cs (str) site symmetry
528	cs+1 (int) site multiplicity
529	cia (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
530	cia+1 (float) Uiso
531	cia+2...cia+7 (6 floats) U11, U22, U33, U12, U13, U23
532	atom[cia+8] (int) unique atom identifier
533
534	============== ====================================================
535
536	.. _Drawing_atoms_table:
537
538	.. index::
539	single: Drawing atoms record description
540	single: Data object descriptions; Drawing atoms record
541
542	----------------------------
543	Drawing Atom Records
544	----------------------------
545
546	If ``phasedict`` points to the phase information in the data tree, then
547	drawing atoms are contained in a list of drawing atom records (list) in
548	``phasedict['Drawing']['Atoms']``. Also needed to read atom information
549	are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
550	which define locations in the atom record, as shown below. Items shown are
551	always present; additional ones for macromolecular phases are marked 'mm',
552	and those for magnetic structures are marked 'mg'
553
554	.. tabularcolumns:: \|l\|p{4.5in}\|
555
556	============== ===================================================================================
557	location explanation
558	============== ===================================================================================
559	ct-4 mm - (str) residue number
560	ct-3 mm - (str) residue name (e.g. ALA)
561	ct-2 mm - (str) chain label
562	ct-1 (str) atom label
563	ct (str) atom type
564	cx,cx+1,cx+2 (3 floats) the x,y and z coordinates
565	cx+3,cx+4,cx+5 mg - (3 floats) atom magnetic moment along a,b,c in Bohr magnetons
566	cs-1 (str) Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1')
567	cs (str) atom drawing style; e.g. 'balls & sticks'
568	cs+1 (str) atom label style (e.g. 'name')
569	cs+2 (int) atom color (RBG triplet)
570	cs+3 (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
571	cs+4 (float) Uiso
572	cs+5...cs+11 (6 floats) U11, U22, U33, U12, U13, U23
573	ci (int) unique atom identifier; matches source atom Id in Atom Records
574	============== ===================================================================================
575
576	.. _Rigid_Body_Insertions:
577
578	----------------------------
579	Rigid Body Insertions
580	----------------------------
581
582	If ``phasedict`` points to the phase information in the data tree, then
583	rigid body information is contained in list(s) in
584	``phasedict['RBModels']['Residue']`` and/or ``phasedict['RBModels']['Vector']``
585	for each rigid body inserted into the current phase.
586
587	.. tabularcolumns:: \|l\|p{4.5in}\|
588
589	============== ===================================================================================
590	key explanation
591	============== ===================================================================================
592	fixOrig Should the origin be fixed (when editing, not the refinement flag)
593	Ids Ids for assignment of atoms in the rigid body
594	numChain Chain number for macromolecular fits
595	Orient Orientation of the RB as a quaternion and a refinement flag (' ', 'A' or 'AV')
596	OrientVec Orientation of the RB expressed as a vector and azimuthal rotation angle
597	Orig Origin of the RB in fractional coordinates and refinement flag (bool)
598	RBId References the unique ID of a rigid body in the
599	:ref:`Rigid Body Objects <RBData_table>`
600	RBname The name for the rigid body (str)
601	AtomFrac The atom fractions for the rigid body
602	ThermalMotion The thermal motion description for the rigid body, which includes a choice for
603	the model and can include TLS parameters or an overall Uiso value.
604	Torsions Defines the torsion angle and refinement flag for each torsion defined in
605	the :ref:`Rigid Body Object <RBData_table>`
606	============== ===================================================================================
607
608	.. _Powder_table:
609
610	.. index::
611	single: Powder data object description
612	single: Data object descriptions; Powder Data
613
614	Powder Diffraction Tree Items
615	-----------------------------
616
617	Every powder diffraction histogram is stored in the GSAS-II data tree
618	with a top-level entry named beginning with the string "PWDR ". The
619	diffraction data for that information are directly associated with
620	that tree item and there are a series of children to that item. The
621	routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
622	and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
623	load this information into a dictionary where the child tree name is
624	used as a key, and the information in the main entry is assigned
625	a key of ``Data``, as outlined below.
626
627	.. tabularcolumns:: \|p{1in}\|p{1in}\|p{4in}\|
628
629	====================== =============== ===========================================================
630	key sub-key explanation
631	====================== =============== ===========================================================
632	Comments \\ (list of str) Text strings extracted from the original powder
633	data header. These cannot be changed by the user;
634	it may be empty.
635	Limits \\ (list) two two element lists, as [[Ld,Hd],[L,H]]
636	where L and Ld are the current and default lowest
637	two-theta value to be used and
638	where H and Hd are the current and default highest
639	two-theta value to be used.
640	Reflection Lists \\ (dict of dicts) with an entry for each phase in the
641	histogram. The contents of each dict item
642	is a dict containing reflections, as described in
643	the :ref:`Powder Reflections <PowderRefl_table>`
644	description.
645	Instrument Parameters \\ (dict) The instrument parameters uses different dicts
646	for the constant wavelength (CW) and time-of-flight (TOF)
647	cases. See below for the descriptions of each.
648	wtFactor \\ (float) A weighting factor to increase or decrease
649	the leverage of data in the histogram .
650	A value of 1.0 weights the data with their
651	standard uncertainties and a larger value
652	increases the weighting of the data (equivalent
653	to decreasing the uncertainties).
654	Sample Parameters \\ (dict) Parameters that describe how
655	the data were collected, as listed
656	below. Refinable parameters are a list containing
657	a float and a bool, where the second value
658	specifies if the value is refined, otherwise
659	the value is a float unless otherwise noted.
660	\\ Scale The histogram scale factor (refinable)
661	\\ Absorption The sample absorption coefficient as
662	:math:`\\mu r` where r is the radius
663	(refinable). Only valid for Debye-Scherrer geometry.
664	\\ SurfaceRoughA Surface roughness parameter A as defined by
665	Surotti, J. Appl. Cryst, 5, 325-331, 1972.
666	(refinable - only valid for Bragg-Brentano geometry)
667	\\ SurfaceRoughB Surface roughness parameter B (refinable -
668	only valid for Bragg-Brentano geometry)
669	\\ DisplaceX, Sample displacement from goniometer center
670	DisplaceY where Y is along the beam direction and
671	X is perpendicular. Units are :math:`\\mu m`
672	(refinable).
673	\\ Phi, Chi, Goniometer sample setting angles, in degrees.
674	Omega
675	\\ Gonio. radius Radius of the diffractometer in mm
676	\\ InstrName (str) A name for the instrument, used in preparing
677	a CIF .
678	\\ Force, Variables that describe how the measurement
679	Temperature, was performed. Not used directly in
680	Humidity, any computations.
681	Pressure,
682	Voltage
683	\\ ranId (int) The random-number Id for the histogram
684	(same value as where top-level key is ranId)
685	\\ Type (str) Type of diffraction data, may be 'Debye-Scherrer'
686	or 'Bragg-Brentano' .
687	hId \\ (int) The number assigned to the histogram when
688	the project is loaded or edited (can change)
689	ranId \\ (int) A random number id for the histogram
690	that does not change
691	Background \\ (list) The background is stored as a list with where
692	the first item in the list is list and the second
693	item is a dict. The list contains the background
694	function and its coefficients; the dict contains
695	Debye diffuse terms and background peaks.
696	(TODO: this needs to be expanded.)
697	Data \\ (list) The data consist of a list of 6 np.arrays
698	containing in order:
699
700	0. the x-postions (two-theta in degrees),
701	1. the intensity values (Yobs),
702	2. the weights for each Yobs value
703	3. the computed intensity values (Ycalc)
704	4. the background values
705	5. Yobs-Ycalc
706	====================== =============== ===========================================================
707
708	.. _CWPowder_table:
709
710	.. index::
711	single: Powder data CW Instrument Parameters
712
713	-----------------------------
714	CW Instrument Parameters
715	-----------------------------
716
717	Instrument Parameters are placed in a list of two dicts,
718	where the keys in the first dict are listed below. Note that the dict contents are different for
719	constant wavelength (CW) vs. time-of-flight (TOF) histograms.
720	The value for each item is a list containing three values: the initial value, the current value
721	and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
722	cannot be refined. The first and second values are floats unless otherwise noted.
723	Items not refined are noted as [*]
724
725	.. tabularcolumns:: \|l\|p{1in}\|p{4in}\|
726
727	======================== =============== ===========================================================
728	key sub-key explanation
729	======================== =============== ===========================================================
730	Instrument Parameters[0] Type [*] (str) Histogram type:
731	* 'PXC' for constant wavelength x-ray
732	* 'PNC' for constant wavelength neutron
733	\\ Bank [*] (int) Data set number in a multidata file (usually 1)
734	\\ Lam (float) Specifies a wavelength in :math:`\\AA`
735	\\ Lam1 [*] (float) Specifies the primary wavelength in
736	:math:`\\AA`, used in place of Lam
737	when an :math:`\\alpha_1, \\alpha_2`
738	source is used.
739	\\ Lam2 [*] (float) Specifies the secondary wavelength in
740	:math:`\\AA`, used with Lam1
741	\\ I(L2)/I(L1) (float) Ratio of Lam2 to Lam1, used with Lam1
742	\\ Zero (float) Two-theta zero correction in degrees
743	\\ Azimuth [*] (float) Azimuthal setting angle for data recorded with differing setting angles
744	\\ U, V, W (float) Cagliotti profile coefficients
745	for Gaussian instrumental broadening, where the
746	FWHM goes as
747	:math:`U \\tan^2\\theta + V \\tan\\theta + W`
748	\\ X, Y, Z (float) Cauchy (Lorentzian) instrumental broadening coefficients
749	\\ SH/L (float) Variant of the Finger-Cox-Jephcoat asymmetric
750	peak broadening ratio. Note that this is the
751	sum of S/L and H/L where S is
752	sample height, H is the slit height and
753	L is the goniometer diameter.
754	\\ Polariz. (float) Polarization coefficient.
755	Instrument Parameters[1] (empty dict)
756	======================== =============== ===========================================================
757
758	.. _TOFPowder_table:
759
760	.. index::
761	single: Powder data TOF Instrument Parameters
762
763	-----------------------------
764	TOF Instrument Parameters
765	-----------------------------
766
767	Instrument Parameters are also placed in a list of two dicts,
768	where the keys in each dict listed below, but here for
769	time-of-flight (TOF) histograms.
770	The value for each item is a list containing three values: the initial value, the current value
771	and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
772	cannot be refined. The first and second values are floats unless otherwise noted.
773	Items not refined are noted as [*]
774
775	.. tabularcolumns:: \|l\|p{1.5in}\|p{4in}\|
776
777	======================== =============== ===========================================================
778	key sub-key explanation
779	======================== =============== ===========================================================
780	Instrument Parameters[0] Type [*] (str) Histogram type:
781	* 'PNT' for time of flight neutron
782	\\ Bank (int) Data set number in a multidata file
783	\\ 2-theta [*] (float) Nominal scattering angle for the detector
784	\\ fltPath [*] (float) Total flight path source-sample-detector
785	\\ Azimuth [*] (float) Azimuth angle for detector right hand rotation
786	from horizontal away from source
787	\\ difC,difA, (float) Diffractometer constants for conversion of d-spacing to TOF
788	difB in microseconds
789	\\ Zero (float) Zero point offset (microseconds)
790	\\ alpha (float) Exponential rise profile coefficients
791	\\ beta-0 (float) Exponential decay profile coefficients
792	beta-1
793	beta-q
794	\\ sig-0 (float) Gaussian profile coefficients
795	sig-1
796	sig-2
797	sig-q
798	\\ X,Y,Z (float) Lorentzian profile coefficients
799	Instrument Parameters[1] Pdabc (list of 4 float lists) Originally created for use in gsas as optional tables
800	of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation
801	from the d-spacing and these tables. The d-true column is apparently unused.
802	======================== =============== ===========================================================
803
804
805	.. _PowderRefl_table:
806
807	.. index::
808	single: Powder reflection object description
809	single: Data object descriptions; Powder Reflections
810
811	Powder Reflection Data Structure
812	--------------------------------
813
814	For every phase in a histogram, the ``Reflection Lists`` value is a dict
815	one element of which is `'RefList'`, which is a np.array containing
816	reflections. The columns in that array are documented below.
817
818	========== ====================================================
819	index explanation
820	========== ====================================================
821	0,1,2 h,k,l (float)
822	3 (int) multiplicity
823	4 (float) d-space, :math:`\\AA`
824	5 (float) pos, two-theta
825	6 (float) sig, Gaussian width
826	7 (float) gam, Lorenzian width
827	8 (float) :math:`F_{obs}^2`
828	9 (float) :math:`F_{calc}^2`
829	10 (float) reflection phase, in degrees
830	11 (float) intensity correction for reflection, this times
831	:math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
832	12 (float) Preferred orientation correction
833	13 (float) Transmission (absorption correction)
834	14 (float) Extinction correction
835	========== ====================================================
836
837	.. _Xtal_table:
838
839	.. index::
840	single: Single Crystal data object description
841	single: Data object descriptions; Single crystal data
842
843	Single Crystal Tree Items
844	-------------------------
845
846	Every single crystal diffraction histogram is stored in the GSAS-II data tree
847	with a top-level entry named beginning with the string "HKLF ". The
848	diffraction data for that information are directly associated with
849	that tree item and there are a series of children to that item. The
850	routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
851	and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
852	load this information into a dictionary where the child tree name is
853	used as a key, and the information in the main entry is assigned
854	a key of ``Data``, as outlined below.
855
856	.. tabularcolumns:: \|l\|l\|p{4in}\|
857
858	====================== =============== ====================================================
859	key sub-key explanation
860	====================== =============== ====================================================
861	Data \\ (dict) that contains the
862	reflection table,
863	as described in the
864	:ref:`Single Crystal Reflections
865	<XtalRefl_table>`
866	description.
867
868	Instrument Parameters \\ (list) containing two dicts where the possible
869	keys in each dict are listed below. The value
870	for most items is a list containing two values:
871	the initial value, the current value.
872	The first and second
873	values are floats unless otherwise noted.
874	\\ Lam (two floats) Specifies a wavelength in :math:`\\AA`
875	\\ Type (two str values) Histogram type :
876	* 'SXC' for constant wavelength x-ray
877	* 'SNC' for constant wavelength neutron
878	* 'SNT' for time of flight neutron
879	\\ InstrName (str) A name for the instrument, used in preparing a CIF
880	wtFactor \\ (float) A weighting factor to increase or decrease
881	the leverage of data in the histogram.
882	A value of 1.0 weights the data with their
883	standard uncertainties and a larger value
884	increases the weighting of the data (equivalent
885	to decreasing the uncertainties).
886
887	hId \\ (int) The number assigned to the histogram when
888	the project is loaded or edited (can change)
889	ranId \\ (int) A random number id for the histogram
890	that does not change
891	====================== =============== ====================================================
892
893	.. _XtalRefl_table:
894
895	.. index::
896	single: Single Crystal reflection object description
897	single: Data object descriptions; Single Crystal Reflections
898
899	Single Crystal Reflection Data Structure
900	----------------------------------------
901
902	For every single crystal a histogram, the ``'Data'`` item contains
903	the structure factors as an np.array in item `'RefList'`.
904	The columns in that array are documented below.
905
906	.. tabularcolumns:: \|l\|p{4in}\|
907
908	========== ====================================================
909	index explanation
910	========== ====================================================
911	0,1,2 (float) h,k,l
912	3 (int) multiplicity
913	4 (float) d-space, :math:`\\AA`
914	5 (float) :math:`F_{obs}^2`
915	6 (float) :math:`\\sigma(F_{obs}^2)`
916	7 (float) :math:`F_{calc}^2`
917	8 (float) :math:`F_{obs}^2T`
918	9 (float) :math:`F_{calc}^2T`
919	10 (float) reflection phase, in degrees
920	11 (float) intensity correction for reflection, this times
921	:math:`F_{obs}^2` or :math:`F_{calc}^2`
922	gives Iobs or Icalc
923	========== ====================================================
924
925	.. _Image_table:
926
927	.. index::
928	image: Image data object description
929	image: Image object descriptions
930
931	Image Data Structure
932	--------------------
933
934	Every 2-dimensional image is stored in the GSAS-II data tree
935	with a top-level entry named beginning with the string "IMG ". The
936	image data are directly associated with that tree item and there
937	are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
938	and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
939	load this information into a dictionary where the child tree name is
940	used as a key, and the information in the main entry is assigned
941	a key of ``Data``, as outlined below.
942
943	.. tabularcolumns:: \|l\|l\|p{4in}\|
944
945	====================== ====================== ====================================================
946	key sub-key explanation
947	====================== ====================== ====================================================
948	Comments \\ (list of str) Text strings extracted from the original image data
949	header or a metafile. These cannot be changed by
950	the user; it may be empty.
951	Image Controls azmthOff (float) The offset to be applied to an azimuthal
952	value. Accomodates
953	detector orientations other than with the detector
954	X-axis
955	horizontal.
956	\\ background image (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
957	during image integration multiplied by value. It must have the same size/shape as
958	the integrated image. NB: value < 0 for subtraction.
959	\\ calibrant (str) The material used for determining the position/orientation
960	of the image. The data is obtained from :func:`ImageCalibrants`
961	and UserCalibrants.py (supplied by user).
962	\\ calibdmin (float) The minimum d-spacing used during the last calibration run.
963	\\ calibskip (int) The number of expected diffraction lines skipped during the last
964	calibration run.
965	\\ center (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
966	strikes the detector plane as determined by calibration. This point
967	does not have to be within the limits of the detector boundaries.
968	\\ centerAzm (bool) If True then the azimuth reported for the integrated slice
969	of the image is at the center line otherwise it is at the leading edge.
970	\\ color (str) The name of the colormap used to display the image. Default = 'Paired'.
971	\\ cutoff (float) The minimum value of I/Ib for a point selected in a diffraction ring for
972	calibration calculations. See pixLimit for details as how point is found.
973	\\ DetDepth (float) Coefficient for penetration correction to distance; accounts for diffraction
974	ring offset at higher angles. Optionally determined by calibration.
975	\\ DetDepthRef (bool) If True then refine DetDepth during calibration/recalibration calculation.
976	\\ distance (float) The distance (mm) from sample to detector plane.
977	\\ ellipses (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
978	center (list) is location (mm) of the ellipse center on the detector plane, phi is the
979	rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
980	radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
981	is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
982	\\ edgemin (float) Not used; parameter in EdgeFinder code.
983	\\ fullIntegrate (bool) If True then integrate over full 360 deg azimuthal range.
984	\\ GonioAngles (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
985	Required for texture calculations.
986	\\ invert_x (bool) If True display the image with the x-axis inverted.
987	\\ invert_y (bool) If True display the image with the y-axis inverted.
988	\\ IOtth (list:floats) The minimum and maximum 2-theta values to be used for integration.
989	\\ LRazimuth (list:floats) The minimum and maximum azimuth values to be used for integration.
990	\\ Oblique (list:float,bool) If True apply a detector absorption correction using the value to the
991	intensities obtained during integration.
992	\\ outAzimuths (int) The number of azimuth pie slices.
993	\\ outChannels (int) The number of 2-theta steps.
994	\\ pixelSize (list:ints) The X,Y dimensions (microns) of each pixel.
995	\\ pixLimit (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
996	This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
997	and subject to cutoff in :func:`GSASIIimage.makeRing`.
998	Locations are used to construct rings of points for calibration calcualtions.
999	\\ PolaVal (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
1000	integration using value.
1001	\\ rings (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
1002	diffraction ring with the same d-spacing (dsp)
1003	\\ ring (list) The x,y coordinates of the >5 points on an inner ring
1004	selected by the user,
1005	\\ Range (list) The minimum & maximum values of the image
1006	\\ rotation (float) The angle between the x-axis and the vector about which the
1007	detector is tilted. Constrained to -180 to 180 deg.
1008	\\ SampleShape (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
1009	calculations.
1010	\\ SampleAbs (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
1011	to cause correction to be applied.
1012	\\ setDefault (bool) If True the use the image controls values for all new images to be read. (might be removed)
1013	\\ setRings (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
1014	\\ showLines (bool) If True then isplay the integration limits to be used.
1015	\\ size (list:int) The number of pixels on the image x & y axes
1016	\\ type (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
1017	\\ tilt (float) The angle the detector normal makes with the incident beam; range -90 to 90.
1018	\\ wavelength (float) The radiation wavelength (:math:`\\AA`) as entered by the user
1019	(or someday obtained from the image header).
1020	Masks Arcs (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
1021	to be excluded from integration
1022	\\ Frames (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
1023	of which is excluded from recalibration and integration. Only one frame is allowed.
1024	\\ Points (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
1025	from integration.
1026	\\ Polygons (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
1027	to be excluded from integration.
1028	\\ Rings (list: lists) Each entry [2-theta,thickness] describes a ring mask
1029	to be excluded from integration.
1030	\\ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
1031	in integrsation. The tuple is the image intensity limits and the list are those set by the user.
1032	\\ SpotMask (dict: int & array)
1033	'esdMul'(int) number of standard deviations above mean ring intensity to mask
1034	'spotMask' (bool array) the spot mask for every pixel in image
1035
1036	Stress/Strain Sample phi (float) Sample rotation about vertical axis.
1037	\\ Sample z (float) Sample translation from the calibration sample position (for Sample phi = 0)
1038	These will be restricted by space group symmetry; result of strain fit refinement.
1039	\\ Type (str) 'True' or 'Conventional': The strain model used for the calculation.
1040	\\ d-zero (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
1041	and are used to determine the strain tensor.
1042	The dictionary items are:
1043	'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
1044	'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
1045	'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
1046	'Esig': (list: float) Esds for Emat from fitting.
1047	'pixLimit': (int) Search range to find highest point on ring for each data point
1048	'cutoff': (float) I/Ib cutoff for searching.
1049	'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
1050	'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
1051	'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
1052
1053	====================== ====================== ====================================================
1054
1055	.. _parmDict_table:
1056
1057	.. index::
1058	single: Parameter dictionary
1059
1060	Parameter Dictionary
1061	-------------------------
1062
1063	The parameter dictionary contains all of the variable parameters for the refinement.
1064	The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
1065	It is prepared in two ways. When loaded from the tree
1066	(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
1067	:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
1068	the values are lists with two elements: ``[value, refine flag]``
1069
1070	When loaded from the GPX file (in
1071	:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
1072	dict is the actual parameter value (usually a float, but sometimes a
1073	letter or string flag value (such as I or A for iso/anisotropic).
1074
1075	Texture implementation
1076	------------------------------
1077
1078	There are two different places where texture can be treated in GSAS-II.
1079	One is for mitigating the effects of texture in a structural refinement.
1080	The other is for texture characterization.
1081
1082	For reducing the effect of texture in a structural refinement
1083	there are entries labeled preferred orientation in each phase's
1084	data tab. Two different approaches can be used for this, the March-Dollase
1085	model and spherical harmonics.
1086
1087	For the March-Dollase model, one axis in reciprocal space is designated as
1088	unique (defaulting to the 001 axis) and reflections are corrected
1089	according to the angle they make with this axis depending on
1090	the March-Dollase ratio. (If unity, no correction is made).
1091	The ratio can be greater than one or less than one depending on if
1092	crystallites oriented along the designated axis are
1093	overrepresented or underrepresented. For most crystal systems there is an
1094	obvious choice for the direction of the unique axis and then only a single
1095	term needs to be refined. If the number is close to 1, then the correction
1096	is not needed.
1097
1098	The second method for reducing the effect of texture in a structural
1099	refinement is to create a crystallite orientation probability surface as an
1100	expansion in terms spherical harmonic functions. Only functions consistent with
1101	cylindrical diffraction suymmetry and having texture symmetry
1102	consistent with the Laue class of phase are used and are allowed,
1103	so the higher the symmetry the fewer terms that are available for a given spherical harmonics order.
1104	To use this correction, select the lowest order that provides
1105	refinable terms and perform a refinement. If the texture index remains close to
1106	one, then the correction is not needed. If a significant improvement is
1107	noted in the profile Rwp, one may wish to see if a higher order expansion
1108	gives an even larger improvement.
1109
1110	To characterize texture in a material, generally one needs data collected with the
1111	sample at multiple orientations or, for TOF, with detectors at multiple
1112	locations around the sample. In this case the detector orientation is given in
1113	each histogram's Sample Parameters and the sample's orientation is described
1114	with the Euler angles specifed on the phase's Texture tab, which is also
1115	where the texture type (cylindrical, rolling,...) and the spherical
1116	harmonic order is selected. This should not be used with a single dataset and
1117	should not be used if the preferred orientations corrections are used.
1118
1119	The coordinate system used for texture characterization is defined where
1120	the sample coordinates (Psi, gamma) are defined with an instrument coordinate
1121	system (I, J, K) such that K is normal to the diffraction plane and J is coincident with the
1122	direction of the incident radiation beam toward the source. We further define
1123	a standard set of right-handed goniometer eulerian angles (Omega, Chi, Phi) so that Omega and Phi are
1124	rotations about K and Chi is a rotation about J when Omega = 0. Finally, as the sample
1125	may be mounted so that the sample coordinate system (Is, Js, Ks) does not coincide with
1126	the instrument coordinate system (I, J, K), we define three eulerian sample rotation angles
1127	(Omega-s, Chi-s, Phi-s) that describe the rotation from (Is, Js, Ks) to (I, J, K). The sample rotation
1128	angles are defined so that with the goniometer angles at zero Omega-s and Phi-s are rotations
1129	about K and Chi-s is a rotation about J.
1130
1131	Three typical examples:
1132
1133	1) Bragg-Brentano laboratory diffractometer: Chi=0
1134	2) Debye-Scherrer counter detector; sample capillary axis perpendicular to diffraction plane: Chi=90
1135	3) Debye-Scherrer 2D area detector positioned directly behind sample; sample capillary axis horizontal; Chi=0
1136
1137	NB: The area detector azimuthal angle will equal 0 in horizontal plane to right as viewed from x-ray source and will equal
1138	90 at vertical "up" direction.
1139
1140	ISODISTORT implementation
1141	------------------------------
1142
1143	CIFs prepared with the ISODISTORT web site
1144	https://stokes.byu.edu/iso/isodistort_version5.6.1/isodistort.php
1145	[B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions."
1146	J. Appl. Cryst. 39, 607-614 (2006).] can be read into GSAS-II using import CIF. This will cause constraints to be established for
1147	structural distortion modes read from the CIF. At present, of the five types of modes only displacive(``_iso_displacivemode``...)
1148	and occupancy (``_iso_occupancymode``...) are processed. Not yet processed: ``_iso_magneticmode``...,
1149	``_iso_rotationalmode``... & ``_iso_strainmode``...
1150
1151	The CIF importer :mod:`G2phase_CIF` implements class :class:`G2phase_CIF.CIFPhaseReader` which offers two methods associated
1152	with ISODISTORT (ID) input. Method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_test` checks to see if a CIF block contains
1153	the loops with ``_iso_displacivemode_label`` or ``_iso_occupancymode_label`` items. If so, method
1154	:meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_proc` is called to read and interpret them. The results are placed into the
1155	reader object's ``.Phase`` class variable as a dict item with key ``'ISODISTORT'``.
1156
1157	Note that each mode ID has a long label with a name such as Pm-3m[1/2,1/2,1/2]R5+(a,a,0)[La:b:dsp]T1u(a). Function
1158	:func:`G2phase_CIF.ISODISTORT_shortLbl` is used to create a short name for this, such as R5_T1u(a) which is made unique
1159	by addition of _n if the short name is duplicated. As each mode is processed, a constraint corresponding to that mode is
1160	created and is added to list in the reader object's ``.Constraints`` class variable. Items placed into that list can either
1161	be a list, which corresponds to a function (new var) type :ref:`constraint definition <Constraints_table>` entry, or an item
1162	can be a dict, which provides help information for each constraint.
1163
1164	------------------------------
1165	Displacive modes
1166	------------------------------
1167
1168	The coordinate variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoVarList']`` and the
1169	corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2VarList']``.
1170	The mode variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoModeList']`` and the
1171	corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2ModeList']``.
1172	[Use ``str(G2VarObj)`` to get the variable name from the G2VarObj object, but note that the phase number, n, for the prefix
1173	"n::" cannot be determined as the phase number is not yet assigned.]
1174
1175	Displacive modes are a bit complex in that they relate to delta displacements, relative to an offset value for each coordinate,
1176	and because the modes are normalized. While GSAS-II also uses displacements, these are added to the coordinates after
1177	each refinement cycle and then the delta values are set to zero.
1178	ISODISTORT uses fixed offsets (subtracted from the actual position
1179	to obtain the delta values) that are taken from the parent structure coordinate and the initial offset value
1180	(in ``_iso_deltacoordinate_value``) and these are placed in
1181	``.Phase['ISODISTORT']['G2coordOffset']`` in the same order as ``.Phase['ISODISTORT']['G2ModeList']`` and
1182	``.Phase['ISODISTORT']['IsoVarList']``.
1183
1184	The normalization factors (which the delta values are divided by)
1185	are taken from ``_iso_displacivemodenorm_value`` and are placed in ``.Phase['ISODISTORT']['NormList']`` in the same
1186	order as as ``...['IsoModeList']`` and ``...['G2ModeList']``.
1187
1188	The CIF contains a sparse matrix, from the ``loop_`` containing ``_iso_displacivemodematrix_value`` which provides the equations
1189	for determining the mode values from the coordinates, that matrix is placed in ``.Phase['ISODISTORT']['Mode2VarMatrix']``.
1190	The matrix is inverted to produce ``.Phase['ISODISTORT']['Var2ModeMatrix']``, which determines how to compute the
1191	mode values from the delta coordinate values. These values are used for the in :func:`GSASIIconstrGUI.ShowIsoDistortCalc`,
1192	which shows coordinate and mode values, the latter with s.u. values.
1193
1194	------------------------------
1195	Occupancy modes
1196	------------------------------
1197
1198
1199	The delta occupancy variables, as named by ISODISTORT, are placed in
1200	``.Phase['ISODISTORT']['OccVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed
1201	in ``.Phase['ISODISTORT']['G2OccVarList']``. The mode variables, as named by ISODISTORT, are placed in
1202	``.Phase['ISODISTORT']['OccModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed
1203	in ``.Phase['ISODISTORT']['G2OccModeList']``.
1204
1205	Occupancy modes, like Displacive modes, are also refined as delta values. However, GSAS-II directly refines the fractional
1206	occupancies. Offset values for each atom, are taken from ``_iso_occupancy_formula`` and are placed in
1207	``.Phase['ISODISTORT']['ParentOcc]``. (Offset values are subtracted from the actual position to obtain the delta values.)
1208	Modes are normalized (where the mode values are divided by the normalization factor) are taken from ``_iso_occupancymodenorm_value``
1209	and are placed in ``.Phase['ISODISTORT']['OccNormList']`` in the same order as as ``...['OccModeList']`` and
1210	``...['G2OccModeList']``.
1211
1212	The CIF contains a sparse matrix, from the ``loop_`` containing ``_iso_occupancymodematrix_value``, which provides the
1213	equations for determining the mode values from the coordinates. That matrix is placed in ``.Phase['ISODISTORT']['Occ2VarMatrix']``.
1214	The matrix is inverted to produce ``.Phase['ISODISTORT']['Var2OccMatrix']``, which determines how to compute the
1215	mode values from the delta coordinate values.
1216
1217
1218	------------------------------
1219	Mode Computations
1220	------------------------------
1221
1222	Constraints are processed after the CIF has been read in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` or
1223	:meth:`GSASIIscriptable.G2Project.add_phase` by moving them from the reader object's ``.Constraints``
1224	class variable to the Constraints tree entry's ['Phase'] list (for list items defining constraints) or
1225	the Constraints tree entry's ['_Explain'] dict (for dict items defining constraint help information)
1226
1227	The information in ``.Phase['ISODISTORT']`` is used in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1228	values, the latter with s.u. values. This can be called from the Constraints and Phase/Atoms tree items.
1229
1230	Before each refinement, constraints are processed as :ref:`described elsewhere <Constraints_processing>`. After a refinement
1231	is complete, :func:`GSASIImapvars.PrintIndependentVars` shows the shifts and s.u.'s on the refined modes,
1232	using GSAS-II values, but :func:`GSASIIstrIO.PrintISOmodes` prints the ISODISTORT modes as computed in the web site.
1233
1234
1235	.. _ParameterLimits:
1236
1237	.. index::
1238	single: Parameter limits
1239
1240	Parameter Limits
1241	------------------------------
1242
1243	One of the most often requested "enhancements" for GSAS-II would be the inclusion
1244	of constraints to force parameters such as occupancies or Uiso values to stay within
1245	expected ranges. While it is possible for users to supply their own restraints that would
1246	perform this by supplying an appropriate expression with the "General" restraints, the
1247	GSAS-II authors do not feel that use of restraints or constraints are a good solution for
1248	this common problem where parameters refine to non-physical values. This is because when
1249	this occurs, most likely one of the following cases is occurring:
1250
1251	#. there is a significant problem
1252	with the model, for example for an x-ray fit if an O atom is placed where a S is actually
1253	present, the Uiso will refine artificially small or the occupancy much larger than unity
1254	to try to compensate for the missing electrons; or
1255
1256	#. the data are simply insensitive
1257	to the parameter or combination of parameters, for example unless very high-Q data
1258	are included, the effects of a occupancy and Uiso value can have compensating effects,
1259	so an assumption must be made; likewise, with neutron data natural-abundance V atoms
1260	are nearly invisible due to weak coherent scattering. No parameters can be fit for a
1261	V atom with neutrons.
1262
1263	#. the parameter is non-physical (such as a negative Uiso value) but within
1264	two sigma (sigma = standard uncertainty, aka e.s.d.) of a reasonable value,
1265	in which case the
1266	value is not problematic as it is experimentally indistinguishable from an
1267	expected value.
1268
1269	#. there is a systematic problem with the data (experimental error)
1270
1271	In all these cases, this situation needs to be reviewed by a crystallographer to decide
1272	how to best determine a structural model for these data. An implementation with a constraint
1273	or restraint is likely to simply hide the problem from the user, making it more probable
1274	that a poor model choice is obtained.
1275
1276	What GSAS-II does implement is to allow users to specify ranges for parameters
1277	that works by disabling
1278	refinement of parameters that refine beyond either a lower limit or an upper limit, where
1279	either or both may be optionally specified. Parameters limits are specified in the Controls
1280	tree entry in dicts named as ``Controls['parmMaxDict']`` and ``Controls['parmMinDict']``, where
1281	the keys are :class:`G2VarObj` objects corresponding to standard GSAS-II variable
1282	(see :func:`getVarDescr` and :func:`CompileVarDesc`) names, where a
1283	wildcard ('*') may optionally be used for histogram number or atom number
1284	(phase number is intentionally not allowed as a wildcard as it makes little sense
1285	to group the same parameter together different phases). Note
1286	that :func:`prmLookup` is used to see if a name matches a wildcard. The upper or lower limit
1287	is placed into these dicts as a float value. These values can be edited using the window
1288	created by the Calculate/"View LS parms" menu command or in scripting with the
1289	:meth:`GSASIIscriptable.G2Project.set_Controls` function.
1290	In the GUI, a checkbox labeled "match all histograms/atoms" is used to insert a wildcard
1291	into the appropriate part of the variable name.
1292
1293	When a refinement is conducted, routine :func:`GSASIIstrMain.dropOOBvars` is used to
1294	find parameters that have refined to values outside their limits. If this occurs, the parameter
1295	is set to the limiting value and the variable name is added to a list of frozen variables
1296	(as a :class:`G2VarObj` objects) kept in a list in the
1297	``Controls['parmFrozen']`` dict. In a sequential refinement, this is kept separate for
1298	each histogram as a list in
1299	``Controls['parmFrozen'][histogram]`` (where the key is the histogram name) or as a list in
1300	``Controls['parmFrozen']['FrozenList']`` for a non-sequential fit.
1301	This allows different variables
1302	to be frozen in each section of a sequential fit.
1303	Frozen parameters are not included in refinements through removal from the
1304	list of parameters to be refined (``varyList``) in :func:`GSASIIstrMain.Refine` or
1305	:func:`GSASIIstrMain.SeqRefine`.
1306	The data window for the Controls tree item shows the number of Frozen variables and
1307	the individual variables can be viewed with the Calculate/"View LS parms" menu window or
1308	obtained with :meth:`GSASIIscriptable.G2Project.get_Frozen`.
1309	Once a variable is frozen, it will not be refined in any
1310	future refinements unless the the variable is removed (manually) from the list. This can also
1311	be done with the Calculate/"View LS parms" menu window or
1312	:meth:`GSASIIscriptable.G2Project.set_Frozen`.
1313
1314
1315	.. seealso::
1316	:class:`G2VarObj`
1317	:func:`getVarDescr`
1318	:func:`CompileVarDesc`
1319	:func:`prmLookup`
1320	:class:`GSASIIctrlGUI.ShowLSParms`
1321	:class:`GSASIIctrlGUI.VirtualVarBox`
1322	:func:`GSASIIstrIO.SetUsedHistogramsAndPhases`
1323	:func:`GSASIIstrIO.SaveUpdatedHistogramsAndPhases`
1324	:func:`GSASIIstrIO.SetSeqResult`
1325	:func:`GSASIIstrMain.dropOOBvars`
1326	:meth:`GSASIIscriptable.G2Project.set_Controls`
1327	:meth:`GSASIIscriptable.G2Project.get_Frozen`
1328	:meth:`GSASIIscriptable.G2Project.set_Frozen`
1329
1330	Classes and routines
1331	----------------------
1332
1333	'''
1334	from __future__ import division, print_function
1335	import platform
1336	import re
1337	import random as ran
1338	import sys
1339	import os.path
1340	if '2' in platform.python_version_tuple()[0]:
1341	import cPickle
1342	else:
1343	import pickle as cPickle
1344	import GSASIIpath
1345	import GSASIImath as G2mth
1346	import GSASIIspc as G2spc
1347	import numpy as np
1348
1349	GSASIIpath.SetVersionNumber("$Revision: 5110 $")
1350
1351	DefaultControls = {
1352	'deriv type':'analytic Hessian',
1353	'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
1354	'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
1355	'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
1356	'Author':'no name','newLeBail':False,
1357	'FreePrm1':'Sample humidity (%)',
1358	'FreePrm2':'Sample voltage (V)',
1359	'FreePrm3':'Applied load (MN)',
1360	'ShowCell':False,
1361	}
1362	'''Values to be used as defaults for the initial contents of the ``Controls``
1363	data tree item.
1364	'''
1365	def StripUnicode(string,subs='.'):
1366	'''Strip non-ASCII characters from strings
1367
1368	:param str string: string to strip Unicode characters from
1369	:param str subs: character(s) to place into string in place of each
1370	Unicode character. Defaults to '.'
1371
1372	:returns: a new string with only ASCII characters
1373	'''
1374	s = ''
1375	for c in string:
1376	if ord(c) < 128:
1377	s += c
1378	else:
1379	s += subs
1380	return s
1381	# return s.encode('ascii','replace')
1382
1383	def MakeUniqueLabel(lbl,labellist):
1384	'''Make sure that every a label is unique against a list by adding
1385	digits at the end until it is not found in list.
1386
1387	:param str lbl: the input label
1388	:param list labellist: the labels that have already been encountered
1389	:returns: lbl if not found in labellist or lbl with ``_1-9`` (or
1390	``_10-99``, etc.) appended at the end
1391	'''
1392	lbl = StripUnicode(lbl.strip(),'_')
1393	if not lbl: # deal with a blank label
1394	lbl = '_1'
1395	if lbl not in labellist:
1396	labellist.append(lbl)
1397	return lbl
1398	i = 1
1399	prefix = lbl
1400	if '_' in lbl:
1401	prefix = lbl[:lbl.rfind('_')]
1402	suffix = lbl[lbl.rfind('_')+1:]
1403	try:
1404	i = int(suffix)+1
1405	except: # suffix could not be parsed
1406	i = 1
1407	prefix = lbl
1408	while prefix+'_'+str(i) in labellist:
1409	i += 1
1410	else:
1411	lbl = prefix+'_'+str(i)
1412	labellist.append(lbl)
1413	return lbl
1414
1415	PhaseIdLookup = {}
1416	'''dict listing phase name and random Id keyed by sequential phase index as a str;
1417	best to access this using :func:`LookupPhaseName`
1418	'''
1419	PhaseRanIdLookup = {}
1420	'''dict listing phase sequential index keyed by phase random Id;
1421	best to access this using :func:`LookupPhaseId`
1422	'''
1423	HistIdLookup = {}
1424	'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
1425	best to access this using :func:`LookupHistName`
1426	'''
1427	HistRanIdLookup = {}
1428	'''dict listing histogram sequential index keyed by histogram random Id;
1429	best to access this using :func:`LookupHistId`
1430	'''
1431	AtomIdLookup = {}
1432	'''dict listing for each phase index as a str, the atom label and atom random Id,
1433	keyed by atom sequential index as a str;
1434	best to access this using :func:`LookupAtomLabel`
1435	'''
1436	AtomRanIdLookup = {}
1437	'''dict listing for each phase the atom sequential index keyed by atom random Id;
1438	best to access this using :func:`LookupAtomId`
1439	'''
1440	ShortPhaseNames = {}
1441	'''a dict containing a possibly shortened and when non-unique numbered
1442	version of the phase name. Keyed by the phase sequential index.
1443	'''
1444	ShortHistNames = {}
1445	'''a dict containing a possibly shortened and when non-unique numbered
1446	version of the histogram name. Keyed by the histogram sequential index.
1447	'''
1448
1449	#VarDesc = {} # removed 1/30/19 BHT as no longer needed (I think)
1450	#''' This dictionary lists descriptions for GSAS-II variables,
1451	#as set in :func:`CompileVarDesc`. See that function for a description
1452	#for how keys and values are written.
1453	#'''
1454
1455	reVarDesc = {}
1456	''' This dictionary lists descriptions for GSAS-II variables where
1457	keys are compiled regular expressions that will match the name portion
1458	of a parameter name. Initialized in :func:`CompileVarDesc`.
1459	'''
1460
1461	reVarStep = {}
1462	''' This dictionary lists the preferred step size for numerical
1463	derivative computation w/r to a GSAS-II variable. Keys are compiled
1464	regular expressions and values are the step size for that parameter.
1465	Initialized in :func:`CompileVarDesc`.
1466	'''
1467	# create a default space group object for P1; N.B. fails when building documentation
1468	try:
1469	P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1470	except:
1471	pass
1472
1473	def GetPhaseNames(fl):
1474	''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1475	NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1476
1477	:param file fl: opened .gpx file
1478	:return: list of phase names
1479	'''
1480	PhaseNames = []
1481	while True:
1482	try:
1483	data = cPickle.load(fl)
1484	except EOFError:
1485	break
1486	datum = data[0]
1487	if 'Phases' == datum[0]:
1488	for datus in data[1:]:
1489	PhaseNames.append(datus[0])
1490	fl.seek(0) #reposition file
1491	return PhaseNames
1492
1493	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1494	'''Create a new phase dict with default values for various parameters
1495
1496	:param str Name: Name for new Phase
1497
1498	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1499	defaults to data for P 1
1500
1501	:param list cell: unit cell parameter list; defaults to
1502	[1.0,1.0,1.0,90.,90,90.,1.]
1503
1504	'''
1505	if SGData is None: SGData = P1SGData
1506	if cell is None: cell=[1.0,1.0,1.0,90.,90.,90.,1.]
1507	phaseData = {
1508	'ranId':ran.randint(0,sys.maxsize),
1509	'General':{
1510	'Name':Name,
1511	'Type':'nuclear',
1512	'Modulated':False,
1513	'AtomPtrs':[3,1,7,9],
1514	'SGData':SGData,
1515	'Cell':[False,]+cell,
1516	'Pawley dmin':1.0,
1517	'Data plot type':'None',
1518	'SH Texture':{
1519	'Order':0,
1520	'Model':'cylindrical',
1521	'Sample omega':[False,0.0],
1522	'Sample chi':[False,0.0],
1523	'Sample phi':[False,0.0],
1524	'SH Coeff':[False,{}],
1525	'SHShow':False,
1526	'PFhkl':[0,0,1],
1527	'PFxyz':[0,0,1],
1528	'PlotType':'Pole figure',
1529	'Penalty':[['',],0.1,False,1.0]}},
1530	'Atoms':[],
1531	'Drawing':{},
1532	'Histograms':{},
1533	'Pawley ref':[],
1534	'RBModels':{},
1535	}
1536	if Super and Super.get('Use',False):
1537	phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1538	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])[1]
1539	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1540
1541	return phaseData
1542
1543	def ReadCIF(URLorFile):
1544	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1545	(from James Hester).
1546	The open routine gets confused with DOS names that begin with a letter and colon
1547	"C:\\dir\" so this routine will try to open the passed name as a file and if that
1548	fails, try it as a URL
1549
1550	:param str URLorFile: string containing a URL or a file name. Code will try first
1551	to open it as a file and then as a URL.
1552
1553	:returns: a PyCifRW CIF object.
1554	'''
1555	import CifFile as cif # PyCifRW from James Hester
1556
1557	# alternate approach:
1558	#import urllib
1559	#ciffile = 'file:'+urllib.pathname2url(filename)
1560
1561	try:
1562	fp = open(URLorFile,'r')
1563	cf = cif.ReadCif(fp)
1564	fp.close()
1565	return cf
1566	except IOError:
1567	return cif.ReadCif(URLorFile)
1568
1569	def TestIndexAll():
1570	'''Test if :func:`IndexAllIds` has been called to index all phases and
1571	histograms (this is needed before :func:`G2VarObj` can be used.
1572
1573	:returns: Returns True if indexing is needed.
1574	'''
1575	if PhaseIdLookup or AtomIdLookup or HistIdLookup:
1576	return False
1577	return True
1578
1579	def IndexAllIds(Histograms,Phases):
1580	'''Scan through the used phases & histograms and create an index
1581	to the random numbers of phases, histograms and atoms. While doing this,
1582	confirm that assigned random numbers are unique -- just in case lightning
1583	strikes twice in the same place.
1584
1585	Note: this code assumes that the atom random Id (ranId) is the last
1586	element each atom record.
1587
1588	This is called when phases & histograms are looked up
1589	in these places (only):
1590
1591	* :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` (which loads the histograms and phases from a GPX file),
1592	* :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree` (which does the same thing but from the data tree.)
1593	* :meth:`~GSASIIdataGUI.GSASII.OnFileClose` (clears out an old project)
1594
1595	Note that globals :data:`PhaseIdLookup` and :data:`PhaseRanIdLookup` are
1596	also set in :func:`AddPhase2Index` to temporarily assign a phase number
1597	as a phase is being imported.
1598
1599	TODO: do we need a lookup for rigid body variables?
1600	'''
1601	# process phases and atoms
1602	PhaseIdLookup.clear()
1603	PhaseRanIdLookup.clear()
1604	AtomIdLookup.clear()
1605	AtomRanIdLookup.clear()
1606	ShortPhaseNames.clear()
1607	for ph in Phases:
1608	cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1609	ranId = Phases[ph]['ranId']
1610	while ranId in PhaseRanIdLookup:
1611	# Found duplicate random Id! note and reassign
1612	print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1613	Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1614	pId = str(Phases[ph]['pId'])
1615	PhaseIdLookup[pId] = (ph,ranId)
1616	PhaseRanIdLookup[ranId] = pId
1617	shortname = ph #[:10]
1618	while shortname in ShortPhaseNames.values():
1619	shortname = ph[:8] + ' ('+ pId + ')'
1620	ShortPhaseNames[pId] = shortname
1621	AtomIdLookup[pId] = {}
1622	AtomRanIdLookup[pId] = {}
1623	for iatm,at in enumerate(Phases[ph]['Atoms']):
1624	ranId = at[cia+8]
1625	while ranId in AtomRanIdLookup[pId]: # check for dups
1626	print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1627	at[cia+8] = ranId = ran.randint(0,sys.maxsize)
1628	AtomRanIdLookup[pId][ranId] = str(iatm)
1629	if Phases[ph]['General']['Type'] == 'macromolecular':
1630	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1631	else:
1632	label = at[ct-1]
1633	AtomIdLookup[pId][str(iatm)] = (label,ranId)
1634	# process histograms
1635	HistIdLookup.clear()
1636	HistRanIdLookup.clear()
1637	ShortHistNames.clear()
1638	for hist in Histograms:
1639	ranId = Histograms[hist]['ranId']
1640	while ranId in HistRanIdLookup:
1641	# Found duplicate random Id! note and reassign
1642	print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1643	Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1644	hId = str(Histograms[hist]['hId'])
1645	HistIdLookup[hId] = (hist,ranId)
1646	HistRanIdLookup[ranId] = hId
1647	shortname = hist[:15]
1648	while shortname in ShortHistNames.values():
1649	shortname = hist[:11] + ' ('+ hId + ')'
1650	ShortHistNames[hId] = shortname
1651
1652	def AddPhase2Index(rdObj,filename):
1653	'''Add a phase to the index during reading
1654	Used where constraints are generated during import (ISODISTORT CIFs)
1655	'''
1656	ranId = rdObj.Phase['ranId']
1657	ph = 'from '+filename # phase is not named yet
1658	if ranId in PhaseRanIdLookup: return
1659	maxph = -1
1660	for r in PhaseRanIdLookup:
1661	maxph = max(maxph,int(PhaseRanIdLookup[r]))
1662	PhaseRanIdLookup[ranId] = pId = str(maxph + 1)
1663	PhaseIdLookup[pId] = (ph,ranId)
1664	shortname = 'from '+ os.path.splitext((os.path.split(filename))[1])[0]
1665	while shortname in ShortPhaseNames.values():
1666	shortname = ph[:8] + ' ('+ pId + ')'
1667	ShortPhaseNames[pId] = shortname
1668	AtomIdLookup[pId] = {}
1669	AtomRanIdLookup[pId] = {}
1670	for iatm,at in enumerate(rdObj.Phase['Atoms']):
1671	ranId = at[-1]
1672	while ranId in AtomRanIdLookup[pId]: # check for dups
1673	print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1674	at[-1] = ranId = ran.randint(0,sys.maxsize)
1675	AtomRanIdLookup[pId][ranId] = str(iatm)
1676	#if Phases[ph]['General']['Type'] == 'macromolecular':
1677	# label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1678	#else:
1679	# label = at[ct-1]
1680	label = at[0]
1681	AtomIdLookup[pId][str(iatm)] = (label,ranId)
1682
1683	def LookupAtomId(pId,ranId):
1684	'''Get the atom number from a phase and atom random Id
1685
1686	:param int/str pId: the sequential number of the phase
1687	:param int ranId: the random Id assigned to an atom
1688
1689	:returns: the index number of the atom (str)
1690	'''
1691	if not AtomRanIdLookup:
1692	raise Exception('Error: LookupAtomId called before IndexAllIds was run')
1693	if pId is None or pId == '':
1694	raise KeyError('Error: phase is invalid (None or blank)')
1695	pId = str(pId)
1696	if pId not in AtomRanIdLookup:
1697	raise KeyError('Error: LookupAtomId does not have phase '+pId)
1698	if ranId not in AtomRanIdLookup[pId]:
1699	raise KeyError('Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']')
1700	return AtomRanIdLookup[pId][ranId]
1701
1702	def LookupAtomLabel(pId,index):
1703	'''Get the atom label from a phase and atom index number
1704
1705	:param int/str pId: the sequential number of the phase
1706	:param int index: the index of the atom in the list of atoms
1707
1708	:returns: the label for the atom (str) and the random Id of the atom (int)
1709	'''
1710	if not AtomIdLookup:
1711	raise Exception('Error: LookupAtomLabel called before IndexAllIds was run')
1712	if pId is None or pId == '':
1713	raise KeyError('Error: phase is invalid (None or blank)')
1714	pId = str(pId)
1715	if pId not in AtomIdLookup:
1716	raise KeyError('Error: LookupAtomLabel does not have phase '+pId)
1717	if index not in AtomIdLookup[pId]:
1718	raise KeyError('Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']')
1719	return AtomIdLookup[pId][index]
1720
1721	def LookupPhaseId(ranId):
1722	'''Get the phase number and name from a phase random Id
1723
1724	:param int ranId: the random Id assigned to a phase
1725	:returns: the sequential Id (pId) number for the phase (str)
1726	'''
1727	if not PhaseRanIdLookup:
1728	raise Exception('Error: LookupPhaseId called before IndexAllIds was run')
1729	if ranId not in PhaseRanIdLookup:
1730	raise KeyError('Error: LookupPhaseId does not have ranId '+str(ranId))
1731	return PhaseRanIdLookup[ranId]
1732
1733	def LookupPhaseName(pId):
1734	'''Get the phase number and name from a phase Id
1735
1736	:param int/str pId: the sequential assigned to a phase
1737	:returns: (phase,ranId) where phase is the name of the phase (str)
1738	and ranId is the random # id for the phase (int)
1739	'''
1740	if not PhaseIdLookup:
1741	raise Exception('Error: LookupPhaseName called before IndexAllIds was run')
1742	if pId is None or pId == '':
1743	raise KeyError('Error: phase is invalid (None or blank)')
1744	pId = str(pId)
1745	if pId not in PhaseIdLookup:
1746	raise KeyError('Error: LookupPhaseName does not have index '+pId)
1747	return PhaseIdLookup[pId]
1748
1749	def LookupHistId(ranId):
1750	'''Get the histogram number and name from a histogram random Id
1751
1752	:param int ranId: the random Id assigned to a histogram
1753	:returns: the sequential Id (hId) number for the histogram (str)
1754	'''
1755	if not HistRanIdLookup:
1756	raise Exception('Error: LookupHistId called before IndexAllIds was run')
1757	if ranId not in HistRanIdLookup:
1758	raise KeyError('Error: LookupHistId does not have ranId '+str(ranId))
1759	return HistRanIdLookup[ranId]
1760
1761	def LookupHistName(hId):
1762	'''Get the histogram number and name from a histogram Id
1763
1764	:param int/str hId: the sequential assigned to a histogram
1765	:returns: (hist,ranId) where hist is the name of the histogram (str)
1766	and ranId is the random # id for the histogram (int)
1767	'''
1768	if not HistIdLookup:
1769	raise Exception('Error: LookupHistName called before IndexAllIds was run')
1770	if hId is None or hId == '':
1771	raise KeyError('Error: histogram is invalid (None or blank)')
1772	hId = str(hId)
1773	if hId not in HistIdLookup:
1774	raise KeyError('Error: LookupHistName does not have index '+hId)
1775	return HistIdLookup[hId]
1776
1777	def fmtVarDescr(varname):
1778	'''Return a string with a more complete description for a GSAS-II variable
1779
1780	:param str varname: A full G2 variable name with 2 or 3 or 4
1781	colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1782
1783	:returns: a string with the description
1784	'''
1785	s,l = VarDescr(varname)
1786	return s+": "+l
1787
1788	def VarDescr(varname):
1789	'''Return two strings with a more complete description for a GSAS-II variable
1790
1791	:param str name: A full G2 variable name with 2 or 3 or 4
1792	colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1793
1794	:returns: (loc,meaning) where loc describes what item the variable is mapped
1795	(phase, histogram, etc.) and meaning describes what the variable does.
1796	'''
1797
1798	# special handling for parameter names without a colon
1799	# for now, assume self-defining
1800	if varname.find(':') == -1:
1801	return "Global",varname
1802
1803	l = getVarDescr(varname)
1804	if not l:
1805	return ("invalid variable name ("+str(varname)+")!"),""
1806	# return "invalid variable name!",""
1807
1808	if not l[-1]:
1809	l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1810
1811	if len(l) == 3: #SASD variable name!
1812	s = 'component:'+l[1]
1813	return s,l[-1]
1814	s = ""
1815	if l[0] is not None and l[1] is not None: # HAP: keep short
1816	if l[2] == "Scale": # fix up ambigous name
1817	l[5] = "Phase fraction"
1818	if l[0] == '*':
1819	lbl = 'Seq. ref.'
1820	else:
1821	lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1822	if l[1] == '*':
1823	hlbl = 'Seq. ref.'
1824	else:
1825	hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1826	if hlbl[:4] == 'HKLF':
1827	hlbl = 'Xtl='+hlbl[5:]
1828	elif hlbl[:4] == 'PWDR':
1829	hlbl = 'Pwd='+hlbl[5:]
1830	else:
1831	hlbl = 'Hist='+hlbl
1832	s = "Ph="+str(lbl)+" * "+str(hlbl)
1833	else:
1834	if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1835	l[5] = "Scale factor"
1836	if l[2] == 'Back': # background parameters are "special", alas
1837	s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1838	l[-1] += ' #'+str(l[3])
1839	elif l[4] is not None: # rigid body parameter or modulation parm
1840	lbl = ShortPhaseNames.get(l[0],'phase?')
1841	if 'RB' in l[2]: #rigid body parm
1842	s = "RB body #"+str(l[3])+" (type "+str(l[4])+") in "+str(lbl) + ','
1843	else: #modulation parm
1844	s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1845	elif l[3] is not None: # atom parameter,
1846	lbl = ShortPhaseNames.get(l[0],'phase?')
1847	try:
1848	albl = LookupAtomLabel(l[0],l[3])[0]
1849	except KeyError:
1850	albl = 'Atom?'
1851	s = "Atom "+str(albl)+" in "+str(lbl)
1852	elif l[0] == '*':
1853	s = "All phases "
1854	elif l[0] is not None:
1855	lbl = ShortPhaseNames.get(l[0],'phase?')
1856	s = "Phase "+str(lbl)
1857	elif l[1] == '*':
1858	s = 'All hists'
1859	elif l[1] is not None:
1860	hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1861	if hlbl[:4] == 'HKLF':
1862	hlbl = 'Xtl='+hlbl[5:]
1863	elif hlbl[:4] == 'PWDR':
1864	hlbl = 'Pwd='+hlbl[5:]
1865	else:
1866	hlbl = 'Hist='+hlbl
1867	s = str(hlbl)
1868	if not s:
1869	s = 'Global'
1870	return s,l[-1]
1871
1872	def getVarDescr(varname):
1873	'''Return a short description for a GSAS-II variable
1874
1875	:param str name: A full G2 variable name with 2 or 3 or 4
1876	colons (<p>:<h>:name[:<a1>][:<a2>])
1877
1878	:returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1879	where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1880	the histogram number and the atom number; `name` will always be
1881	a str; and `description` is str or `None`.
1882	If the variable name is incorrectly formed (for example, wrong
1883	number of colons), `None` is returned instead of a list.
1884	'''
1885	l = varname.split(':')
1886	if len(l) == 2: #SASD parameter name
1887	return varname,l[0],getDescr(l[1])
1888	if len(l) == 3:
1889	l += [None,None]
1890	elif len(l) == 4:
1891	l += [None]
1892	elif len(l) != 5:
1893	return None
1894	for i in (0,1,3,4):
1895	if l[i] == "":
1896	l[i] = None
1897	l += [getDescr(l[2])]
1898	return l
1899
1900	def CompileVarDesc():
1901	'''Set the values in the variable lookup tables
1902	(:attr:`reVarDesc` and :attr:`reVarStep`).
1903	This is called in :func:`getDescr` and :func:`getVarStep` so this
1904	initialization is always done before use.
1905
1906	Note that keys may contain regular expressions, where '[xyz]'
1907	matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range
1908	of values). '.*' matches any string. For example::
1909
1910	'AUiso':'Atomic isotropic displacement parameter',
1911
1912	will match variable ``'p::AUiso:a'``.
1913	If parentheses are used in the key, the contents of those parentheses can be
1914	used in the value, such as::
1915
1916	'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1917
1918	will match ``AU11``, ``AU23``,... and `U11`, `U23` etc will be displayed
1919	in the value when used.
1920
1921	'''
1922	if reVarDesc: return # already done
1923	for key,value in {
1924	# derived or other sequential vars
1925	'([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1926	u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1927	u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1928	u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1929	# ambiguous, alas:
1930	'Scale' : 'Phase or Histogram scale factor',
1931	# Phase vars (p::<var>)
1932	'A([0-5])' : ('Reciprocal metric tensor component \\1',1e-5),
1933	'[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1934	# Atom vars (p::<var>:a)
1935	'dA([xyz])$' : ('change to atomic coordinate, \\1',1e-6),
1936	'A([xyz])$' : '\\1 fractional atomic coordinate',
1937	'AUiso':('Atomic isotropic displacement parameter',1e-4),
1938	'AU([123][123])':('Atomic anisotropic displacement parameter U\\1',1e-4),
1939	'Afrac': ('Atomic site fraction parameter',1e-5),
1940	'Amul': 'Atomic site multiplicity value',
1941	'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1942	# Hist (:h:<var>) & Phase (HAP) vars (p:h:<var>)
1943	'Back': 'Background term',
1944	'BkPkint;(.*)':'Background peak #\\1 intensity',
1945	'BkPkpos;(.*)':'Background peak #\\1 position',
1946	'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1947	'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1948	# 'Back File' : 'Background file name',
1949	'BF mult' : 'Background file multiplier',
1950	'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1951	'D([123][123])' : 'Anisotropic strain coef. \\1',
1952	'Extinction' : 'Extinction coef.',
1953	'MD' : 'March-Dollase coef.',
1954	'Mustrain;.*' : 'Microstrain coef.',
1955	'Size;.*' : 'Crystallite size value',
1956	'eA$' : 'Cubic mustrain value',
1957	'Ep$' : 'Primary extinction',
1958	'Es$' : 'Secondary type II extinction',
1959	'Eg$' : 'Secondary type I extinction',
1960	'Flack' : 'Flack parameter',
1961	'TwinFr' : 'Twin fraction',
1962	'Layer Disp' : 'Layer displacement along beam',
1963	#Histogram vars (:h:<var>)
1964	'Absorption' : 'Absorption coef.',
1965	'LayerDisp' : 'Bragg-Brentano Layer displacement',
1966	'Displace([XY])' : ('Debye-Scherrer sample displacement \\1',0.1),
1967	'Lam' : ('Wavelength',1e-6),
1968	'I\\(L2\\)\\/I\\(L1\\)' : ('Ka2/Ka1 intensity ratio',0.001),
1969	'Polariz\\.' : ('Polarization correction',1e-3),
1970	'SH/L' : ('FCJ peak asymmetry correction',1e-4),
1971	'([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),
1972	'([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),
1973	'Zero' : 'Debye-Scherrer zero correction',
1974	'Shift' : 'Bragg-Brentano sample displ.',
1975	'SurfRoughA' : 'Bragg-Brenano surface roughness A',
1976	'SurfRoughB' : 'Bragg-Brenano surface roughness B',
1977	'Transparency' : 'Bragg-Brentano sample tranparency',
1978	'DebyeA' : 'Debye model amplitude',
1979	'DebyeR' : 'Debye model radius',
1980	'DebyeU' : 'Debye model Uiso',
1981	'RBV.*' : 'Vector rigid body parameter',
1982	'RBVO([aijk])' : 'Vector rigid body orientation parameter \\1',
1983	'RBVP([xyz])' : 'Vector rigid body \\1 position parameter',
1984	'RBVf' : 'Vector rigid body site fraction',
1985	'RBV([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1986	'RBVU' : 'Residue rigid body group Uiso param.',
1987	'RBRO([aijk])' : 'Residue rigid body orientation parameter \\1',
1988	'RBRP([xyz])' : 'Residue rigid body \\1 position parameter',
1989	'RBRTr;.*' : 'Residue rigid body torsion parameter',
1990	'RBRf' : 'Residue rigid body site fraction',
1991	'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1992	'RBRU' : 'Residue rigid body group Uiso param.',
1993	'constr([0-9]*)' : 'Parameter from constraint',
1994	'nv-([^_]+)_*' : 'New variable constraint parameter named \\1',
1995	# supersymmetry parameters p::<var>:a:o 'Flen','Fcent'?
1996	'mV([0-2])$' : 'Modulation vector component \\1',
1997	'Fsin' : 'Sin site fraction modulation',
1998	'Fcos' : 'Cos site fraction modulation',
1999	'Fzero' : 'Crenel function offset', #may go away
2000	'Fwid' : 'Crenel function width',
2001	'Tmin' : 'ZigZag/Block min location',
2002	'Tmax' : 'ZigZag/Block max location',
2003	'([XYZ])max': 'ZigZag/Block max value for \\1',
2004	'([XYZ])sin' : 'Sin position wave for \\1',
2005	'([XYZ])cos' : 'Cos position wave for \\1',
2006	'U([123][123])sin$' : 'Sin thermal wave for U\\1',
2007	'U([123][123])cos$' : 'Cos thermal wave for U\\1',
2008	'M([XYZ])sin$' : 'Sin mag. moment wave for \\1',
2009	'M([XYZ])cos$' : 'Cos mag. moment wave for \\1',
2010	# PDF peak parms (l:<var>;l = peak no.)
2011	'PDFpos' : 'PDF peak position',
2012	'PDFmag' : 'PDF peak magnitude',
2013	'PDFsig' : 'PDF peak std. dev.',
2014	# SASD vars (l:<var>;l = component)
2015	'Aspect ratio' : 'Particle aspect ratio',
2016	'Length' : 'Cylinder length',
2017	'Diameter' : 'Cylinder/disk diameter',
2018	'Thickness' : 'Disk thickness',
2019	'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
2020	'Dist' : 'Interparticle distance',
2021	'VolFr' : 'Dense scatterer volume fraction',
2022	'epis' : 'Sticky sphere epsilon',
2023	'Sticky' : 'Stickyness',
2024	'Depth' : 'Well depth',
2025	'Width' : 'Well width',
2026	'Volume' : 'Particle volume',
2027	'Radius' : 'Sphere/cylinder/disk radius',
2028	'Mean' : 'Particle mean radius',
2029	'StdDev' : 'Standard deviation in Mean',
2030	'G$': 'Guinier prefactor',
2031	'Rg$': 'Guinier radius of gyration',
2032	'B$': 'Porod prefactor',
2033	'P$': 'Porod power',
2034	'Cutoff': 'Porod cutoff',
2035	'PkInt': 'Bragg peak intensity',
2036	'PkPos': 'Bragg peak position',
2037	'PkSig': 'Bragg peak sigma',
2038	'PkGam': 'Bragg peak gamma',
2039	'e([12][12])' : 'strain tensor e\\1', # strain vars e11, e22, e12
2040	'Dcalc': 'Calc. d-spacing',
2041	'Back$': 'background parameter',
2042	'pos$': 'peak position',
2043	'int$': 'peak intensity',
2044	'WgtFrac':'phase weight fraction',
2045	'alpha':'TOF profile term',
2046	'alpha-[01]':'Pink profile term',
2047	'beta-[01q]':'TOF/Pink profile term',
2048	'sig-[012q]':'TOF profile term',
2049	'dif[ABC]':'TOF to d-space calibration',
2050	'C\\([0-9],[0-9]\\)' : 'spherical harmonics preferred orientation coef.',
2051	'Pressure': 'Pressure level for measurement in MPa',
2052	'Temperature': 'T value for measurement, K',
2053	'FreePrm([123])': 'User defined measurement parameter \\1',
2054	'Gonio. radius': 'Distance from sample to detector, mm',
2055	}.items():
2056	# Needs documentation: HAP: LeBail, newLeBail
2057	# hist: Azimuth, Chi, Omega, Phi, Bank, nDebye, nPeaks
2058
2059	if len(value) == 2:
2060	#VarDesc[key] = value[0]
2061	reVarDesc[re.compile(key)] = value[0]
2062	reVarStep[re.compile(key)] = value[1]
2063	else:
2064	#VarDesc[key] = value
2065	reVarDesc[re.compile(key)] = value
2066
2067	def removeNonRefined(parmList):
2068	'''Remove items from variable list that are not refined and should not
2069	appear as options for constraints
2070
2071	:param list parmList: a list of strings of form "p:h:VAR:a" where
2072	VAR is the variable name
2073
2074	:returns: a list after removing variables where VAR matches a
2075	entry in local variable NonRefinedList
2076	'''
2077	NonRefinedList = ['Omega','Type','Chi','Phi', 'Azimuth','Gonio. radius',
2078	'Lam1','Lam2','Back','Temperature','Pressure',
2079	'FreePrm1','FreePrm2','FreePrm3',
2080	'Source','nPeaks','LeBail','newLeBail','Bank',
2081	'nDebye', #'',
2082	]
2083	return [prm for prm in parmList if prm.split(':')[2] not in NonRefinedList]
2084
2085	def getDescr(name):
2086	'''Return a short description for a GSAS-II variable
2087
2088	:param str name: The descriptive part of the variable name without colons (:)
2089
2090	:returns: a short description or None if not found
2091	'''
2092
2093	CompileVarDesc() # compile the regular expressions, if needed
2094	for key in reVarDesc:
2095	m = key.match(name)
2096	if m:
2097	reVarDesc[key]
2098	return m.expand(reVarDesc[key])
2099	return None
2100
2101	def getVarStep(name,parmDict=None):
2102	'''Return a step size for computing the derivative of a GSAS-II variable
2103
2104	:param str name: A complete variable name (with colons, :)
2105	:param dict parmDict: A dict with parameter values or None (default)
2106
2107	:returns: a float that should be an appropriate step size, either from
2108	the value supplied in :func:`CompileVarDesc` or based on the value for
2109	name in parmDict, if supplied. If not found or the value is zero,
2110	a default value of 1e-5 is used. If parmDict is None (default) and
2111	no value is provided in :func:`CompileVarDesc`, then None is returned.
2112	'''
2113	CompileVarDesc() # compile the regular expressions, if needed
2114	for key in reVarStep:
2115	m = key.match(name)
2116	if m:
2117	return reVarStep[key]
2118	if parmDict is None: return None
2119	val = parmDict.get(key,0.0)
2120	if abs(val) > 0.05:
2121	return abs(val)/1000.
2122	else:
2123	return 1e-5
2124
2125	def GenWildCard(varlist):
2126	'''Generate wildcard versions of G2 variables. These introduce '*'
2127	for a phase, histogram or atom number (but only for one of these
2128	fields) but only when there is more than one matching variable in the
2129	input variable list. So if the input is this::
2130
2131	varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
2132
2133	then the output will be this::
2134
2135	wildList = ['::AUiso:0', '0::AUiso:']
2136
2137	:param list varlist: an input list of GSAS-II variable names
2138	(such as 0::AUiso:0)
2139
2140	:returns: wildList, the generated list of wild card variable names.
2141	'''
2142	wild = []
2143	for i in (0,1,3):
2144	currentL = varlist[:]
2145	while currentL:
2146	item1 = currentL.pop(0)
2147	i1splt = item1.split(':')
2148	if i >= len(i1splt): continue
2149	if i1splt[i]:
2150	nextL = []
2151	i1splt[i] = '[0-9]+'
2152	rexp = re.compile(':'.join(i1splt))
2153	matchlist = [item1]
2154	for nxtitem in currentL:
2155	if rexp.match(nxtitem):
2156	matchlist += [nxtitem]
2157	else:
2158	nextL.append(nxtitem)
2159	if len(matchlist) > 1:
2160	i1splt[i] = '*'
2161	wild.append(':'.join(i1splt))
2162	currentL = nextL
2163	return wild
2164
2165	def LookupWildCard(varname,varlist):
2166	'''returns a list of variable names from list varname
2167	that match wildcard name in varname
2168
2169	:param str varname: a G2 variable name containing a wildcard
2170	(such as \\*::var)
2171	:param list varlist: the list of all variable names used in
2172	the current project
2173	:returns: a list of matching GSAS-II variables (may be empty)
2174	'''
2175	rexp = re.compile(varname.replace('*','[0-9]+'))
2176	return sorted([var for var in varlist if rexp.match(var)])
2177
2178	def prmLookup(name,prmDict):
2179	'''Looks for a parameter in a min/max dictionary, optionally
2180	considering a wild card for histogram or atom number (use of
2181	both will never occur at the same time).
2182
2183	:param name: a GSAS-II parameter name (str, see :func:`getVarDescr`
2184	and :func:`CompileVarDesc`) or a :class:`G2VarObj` object.
2185	:param dict prmDict: a min/max dictionary, (parmMinDict
2186	or parmMaxDict in Controls) where keys are :class:`G2VarObj`
2187	objects.
2188	:returns: Two values, (matchname, value), are returned where:
2189
2190	* matchname (str) is the :class:`G2VarObj` object
2191	corresponding to the actual matched name,
2192	which could contain a wildcard even if name does not; and
2193	* value (float) which contains the parameter limit.
2194	'''
2195	for key,value in prmDict.items():
2196	if str(key) == str(name): return key,value
2197	if key == name: return key,value
2198	return None,None
2199
2200
2201	def _lookup(dic,key):
2202	'''Lookup a key in a dictionary, where None returns an empty string
2203	but an unmatched key returns a question mark. Used in :class:`G2VarObj`
2204	'''
2205	if key is None:
2206	return ""
2207	elif key == "*":
2208	return "*"
2209	else:
2210	return dic.get(key,'?')
2211
2212	def SortVariables(varlist):
2213	'''Sorts variable names in a sensible manner
2214	'''
2215	def cvnnums(var):
2216	v = []
2217	for i in var.split(':'):
2218	# if i == '' or i == '*':
2219	# v.append(-1)
2220	# continue
2221	try:
2222	v.append(int(i))
2223	except:
2224	v.append(-1)
2225	return v
2226	return sorted(varlist,key=cvnnums)
2227
2228	class G2VarObj(object):
2229	'''Defines a GSAS-II variable either using the phase/atom/histogram
2230	unique Id numbers or using a character string that specifies
2231	variables by phase/atom/histogram number (which can change).
2232	Note that :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`,
2233	which calls :func:`IndexAllIds` (or
2234	:func:`GSASIIscriptable.G2Project.index_ids`) should be used to
2235	(re)load the current Ids
2236	before creating or later using the G2VarObj object.
2237
2238	This can store rigid body variables, but does not translate the residue # and
2239	body # to/from random Ids
2240
2241	A :class:`G2VarObj` object can be created with a single parameter:
2242
2243	:param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
2244	object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
2245
2246	* p is the phase number (which may be left blank or may be '*' to indicate all phases);
2247	* h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
2248	* a is the atom number (which may be left blank in which case the third colon is omitted).
2249	The atom number can be specified as '' if a phase number is specified (not as '').
2250	For rigid body variables, specify a will be a string of form "residue:body#"
2251
2252	Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
2253	Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
2254	and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
2255	For a rigid body variables, AtomID is a string of form "residue:body#".
2256
2257	If four positional arguments are supplied, they are:
2258
2259	:param str/int phasenum: The number for the phase (or None or '*')
2260	:param str/int histnum: The number for the histogram (or None or '*')
2261	:param str varname: a single value can be used to create a :class:`G2VarObj`
2262	:param str/int atomnum: The number for the atom (or None or '*')
2263
2264	'''
2265	IDdict = {}
2266	IDdict['phases'] = {}
2267	IDdict['hists'] = {}
2268	IDdict['atoms'] = {}
2269	def __init__(self,*args):
2270	self.phase = None
2271	self.histogram = None
2272	self.name = ''
2273	self.atom = None
2274	if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
2275	# single arg with 4 values
2276	self.phase,self.histogram,self.name,self.atom = args[0]
2277	elif len(args) == 1 and ':' in args[0]:
2278	#parse a string
2279	lst = args[0].split(':')
2280	if lst[0] == '*':
2281	self.phase = '*'
2282	if len(lst) > 3:
2283	self.atom = lst[3]
2284	self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2285	elif lst[1] == '*':
2286	self.histogram = '*'
2287	self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2288	else:
2289	self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2290	self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2291	if len(lst) == 4:
2292	if lst[3] == '*':
2293	self.atom = '*'
2294	else:
2295	self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
2296	elif len(lst) == 5:
2297	self.atom = lst[3]+":"+lst[4]
2298	elif len(lst) == 3:
2299	pass
2300	else:
2301	raise Exception("Incorrect number of colons in var name "+str(args[0]))
2302	self.name = lst[2]
2303	elif len(args) == 4:
2304	if args[0] == '*':
2305	self.phase = '*'
2306	self.atom = args[3]
2307	else:
2308	self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
2309	if args[3] == '*':
2310	self.atom = '*'
2311	elif args[0] is not None:
2312	self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
2313	if args[1] == '*':
2314	self.histogram = '*'
2315	else:
2316	self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
2317	self.name = args[2]
2318	else:
2319	raise Exception("Incorrectly called GSAS-II parameter name")
2320
2321	#print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
2322
2323	def __str__(self):
2324	return self.varname()
2325
2326	def __hash__(self):
2327	'Allow G2VarObj to be a dict key by implementing hashing'
2328	return hash(self.varname())
2329
2330	def varname(self,hist=None):
2331	'''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
2332	string (p:h:<var>:a) or (p:h:<var>)
2333
2334	:param str/int hist: if specified, overrides the histogram number
2335	with the specified value
2336	:returns: the variable name as a str
2337	'''
2338	a = ""
2339	if self.phase == "*":
2340	ph = "*"
2341	if self.atom:
2342	a = ":" + str(self.atom)
2343	else:
2344	ph = _lookup(PhaseRanIdLookup,self.phase)
2345	if self.atom == '*':
2346	a = ':*'
2347	elif self.atom:
2348	if ":" in str(self.atom):
2349	a = ":" + str(self.atom)
2350	elif ph in AtomRanIdLookup:
2351	a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
2352	else:
2353	a = ":?"
2354	if hist is not None and self.histogram:
2355	hist = str(hist)
2356	elif self.histogram == "*":
2357	hist = "*"
2358	else:
2359	hist = _lookup(HistRanIdLookup,self.histogram)
2360	s = (ph + ":" + hist + ":" + str(self.name)) + a
2361	return s
2362
2363	def __repr__(self):
2364	'''Return the detailed contents of the object
2365	'''
2366	s = "<"
2367	if self.phase == '*':
2368	s += "Phases: all; "
2369	if self.atom is not None:
2370	if ":" in str(self.atom):
2371	s += "Rigid body" + str(self.atom) + "; "
2372	else:
2373	s += "Atom #" + str(self.atom) + "; "
2374	elif self.phase is not None:
2375	ph = _lookup(PhaseRanIdLookup,self.phase)
2376	s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
2377	if self.atom == '*':
2378	s += "Atoms: all; "
2379	elif ":" in str(self.atom):
2380	s += "Rigid body" + str(self.atom) + "; "
2381	elif self.atom is not None:
2382	s += "Atom rId=" + str(self.atom)
2383	if ph in AtomRanIdLookup:
2384	s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
2385	else:
2386	s += " (#? -- not found!); "
2387	if self.histogram == '*':
2388	s += "Histograms: all; "
2389	elif self.histogram is not None:
2390	hist = _lookup(HistRanIdLookup,self.histogram)
2391	s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
2392	s += 'Variable name="' + str(self.name) + '">'
2393	return s+" ("+self.varname()+")"
2394
2395	def __eq__(self, other):
2396	'''Allow comparison of G2VarObj to other G2VarObj objects or strings.
2397	If any field is a wildcard ('*') that field matches.
2398	'''
2399	if type(other) is str:
2400	other = G2VarObj(other)
2401	elif type(other) is not G2VarObj:
2402	raise Exception("Invalid type ({}) for G2VarObj comparison with {}"
2403	.format(type(other),other))
2404	if self.phase != other.phase and self.phase != '' and other.phase != '':
2405	return False
2406	if self.histogram != other.histogram and self.histogram != '' and other.histogram != '':
2407	return False
2408	if self.atom != other.atom and self.atom != '' and other.atom != '':
2409	return False
2410	if self.name != other.name:
2411	return False
2412	return True
2413
2414	def fmtVarByMode(self, seqmode, note, warnmsg):
2415	'''Format a parameter object for display. Note that these changes
2416	are only temporary and are only shown only when the Constraints
2417	data tree is selected.
2418
2419	* In a non-sequential refinement or where the mode is 'use-all', the
2420	name is converted unchanged to a str
2421	* In a sequential refinement when the mode is 'wildcards-only' the
2422	name is converted unchanged to a str but a warning is added
2423	for non-wildcarded HAP or Histogram parameters
2424	* In a sequential refinement or where the mode is 'auto-wildcard',
2425	a histogram number is converted to a wildcard (*) and then
2426	converted to str
2427
2428	:param str mode: the sequential mode (see above)
2429	:param str note: value displayed on the line of the constraint/equiv.
2430	:param str warnmsg: a message saying the constraint is not used
2431
2432	:returns: varname, explain, note, warnmsg (all str values) where:
2433
2434	* varname is the parameter expressed as a string,
2435	* explain is blank unless there is a warning explanation about
2436	the parameter or blank
2437	* note is the previous value unless overridden
2438	* warnmsg is the previous value unless overridden
2439	'''
2440	explain = ''
2441	s = self.varname()
2442	if seqmode == 'auto-wildcard':
2443	if self.histogram: s = self.varname('*')
2444	elif seqmode == 'wildcards-only' and self.histogram:
2445	if self.histogram != '*':
2446	warnmsg = 'Ignored due to use of a non-wildcarded histogram number'
2447	note = 'Ignored'
2448	explain = '\nIgnoring: '+self.varname()+' does not contain a wildcard.\n'
2449	elif seqmode != 'use-all' and seqmode != 'wildcards-only':
2450	print('Unexpected mode',seqmode,' in fmtVarByMode')
2451	return s,explain,note,warnmsg
2452
2453	def _show(self):
2454	'For testing, shows the current lookup table'
2455	print ('phases'+ self.IDdict['phases'])
2456	print ('hists'+ self.IDdict['hists'])
2457	print ('atomDict'+ self.IDdict['atoms'])
2458
2459	#==========================================================================
2460	def SetDefaultSample():
2461	'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
2462	return {
2463	'InstrName':'',
2464	'ranId':ran.randint(0,sys.maxsize),
2465	'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
2466	'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],
2467	'Temperature':300.,'Pressure':0.1,'Time':0.0,
2468	'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
2469	'Gonio. radius':200.0,
2470	'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
2471	#SASD items
2472	'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
2473	'Thick':1.0,'Contrast':[0.0,0.0], #contrast & anomalous contrast
2474	'Trans':1.0, #measured transmission
2475	'SlitLen':0.0, #Slit length - in Q(A-1)
2476	}
2477	######################################################################
2478	class ImportBaseclass(object):
2479	'''Defines a base class for the reading of input files (diffraction
2480	data, coordinates,...). See :ref:`Writing a Import Routine<import_routines>`
2481	for an explanation on how to use a subclass of this class.
2482	'''
2483	class ImportException(Exception):
2484	'''Defines an Exception that is used when an import routine hits an expected error,
2485	usually in .Reader.
2486
2487	Good practice is that the Reader should define a value in self.errors that
2488	tells the user some information about what is wrong with their file.
2489	'''
2490	pass
2491
2492	UseReader = True # in __init__ set value of self.UseReader to False to skip use of current importer
2493	def __init__(self,formatName,longFormatName=None,
2494	extensionlist=[],strictExtension=False,):
2495	self.formatName = formatName # short string naming file type
2496	if longFormatName: # longer string naming file type
2497	self.longFormatName = longFormatName
2498	else:
2499	self.longFormatName = formatName
2500	# define extensions that are allowed for the file type
2501	# for windows, remove any extensions that are duplicate, as case is ignored
2502	if sys.platform == 'windows' and extensionlist:
2503	extensionlist = list(set([s.lower() for s in extensionlist]))
2504	self.extensionlist = extensionlist
2505	# If strictExtension is True, the file will not be read, unless
2506	# the extension matches one in the extensionlist
2507	self.strictExtension = strictExtension
2508	self.errors = ''
2509	self.warnings = ''
2510	self.SciPy = False #image reader needed scipy
2511	# used for readers that will use multiple passes to read
2512	# more than one data block
2513	self.repeat = False
2514	self.selections = []
2515	self.repeatcount = 0
2516	self.readfilename = '?'
2517	self.scriptable = False
2518	#print 'created',self.__class__
2519
2520	def ReInitialize(self):
2521	'Reinitialize the Reader to initial settings'
2522	self.errors = ''
2523	self.warnings = ''
2524	self.SciPy = False #image reader needed scipy
2525	self.repeat = False
2526	self.repeatcount = 0
2527	self.readfilename = '?'
2528
2529
2530	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
2531	# '''This method must be supplied in the child class to read the file.
2532	# if the read fails either return False or raise an Exception
2533	# preferably of type ImportException.
2534	# '''
2535	# #start reading
2536	# raise ImportException("Error occurred while...")
2537	# self.errors += "Hint for user on why the error occur
2538	# return False # if an error occurs
2539	# return True # if read OK
2540
2541	def ExtensionValidator(self, filename):
2542	'''This methods checks if the file has the correct extension
2543
2544	:returns:
2545
2546	* False if this filename will not be supported by this reader (only
2547	when strictExtension is True)
2548	* True if the extension matches the list supplied by the reader
2549	* None if the reader allows un-registered extensions
2550
2551	'''
2552	if filename:
2553	ext = os.path.splitext(filename)[1]
2554	if not ext and self.strictExtension: return False
2555	for ext in self.extensionlist:
2556	if sys.platform == 'windows':
2557	if filename.lower().endswith(ext): return True
2558	else:
2559	if filename.endswith(ext): return True
2560	if self.strictExtension:
2561	return False
2562	else:
2563	return None
2564
2565	def ContentsValidator(self, filename):
2566	'''This routine will attempt to determine if the file can be read
2567	with the current format.
2568	This will typically be overridden with a method that
2569	takes a quick scan of [some of]
2570	the file contents to do a "sanity" check if the file
2571	appears to match the selected format.
2572	the file must be opened here with the correct format (binary/text)
2573	'''
2574	#filepointer.seek(0) # rewind the file pointer
2575	return True
2576
2577	def CIFValidator(self, filepointer):
2578	'''A :meth:`ContentsValidator` for use to validate CIF files.
2579	'''
2580	filepointer.seek(0)
2581	for i,l in enumerate(filepointer):
2582	if i >= 1000: return True
2583	'''Encountered only blank lines or comments in first 1000
2584	lines. This is unlikely, but assume it is CIF anyway, since we are
2585	even less likely to find a file with nothing but hashes and
2586	blank lines'''
2587	line = l.strip()
2588	if len(line) == 0: # ignore blank lines
2589	continue
2590	elif line.startswith('#'): # ignore comments
2591	continue
2592	elif line.startswith('data_'): # on the right track, accept this file
2593	return True
2594	else: # found something invalid
2595	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
2596	if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
2597	self.errors += ' '+str(l)
2598	else:
2599	self.errors += ' (binary)'
2600	self.errors += '\n Note: a CIF should only have blank lines or comments before'
2601	self.errors += '\n a data_ statement begins a block.'
2602	return False
2603
2604	######################################################################
2605	class ImportPhase(ImportBaseclass):
2606	'''Defines a base class for the reading of files with coordinates
2607
2608	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
2609	in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` and in
2610	:func:`GSASIIscriptable.import_generic`.
2611	See :ref:`Writing a Import Routine<import_routines>`
2612	for an explanation on how to use this class.
2613
2614	'''
2615	def __init__(self,formatName,longFormatName=None,extensionlist=[],
2616	strictExtension=False,):
2617	# call parent __init__
2618	ImportBaseclass.__init__(self,formatName,longFormatName,
2619	extensionlist,strictExtension)
2620	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
2621	self.SymOps = {} # specified when symmetry ops are in file (e.g. CIF)
2622	self.Constraints = None
2623
2624	######################################################################
2625	class ImportStructFactor(ImportBaseclass):
2626	'''Defines a base class for the reading of files with tables
2627	of structure factors.
2628
2629	Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
2630	which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
2631	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2632	:meth:`Reader`.
2633
2634	See :ref:`Writing a Import Routine<import_routines>`
2635	for an explanation on how to use import classes in general. The specifics
2636	for reading a structure factor histogram require that
2637	the ``Reader()`` routine in the import
2638	class need to do only a few things: It
2639	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2640	and set :attr:`Parameters` with the instrument parameters
2641	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2642	'''
2643	def __init__(self,formatName,longFormatName=None,extensionlist=[],
2644	strictExtension=False,):
2645	ImportBaseclass.__init__(self,formatName,longFormatName,
2646	extensionlist,strictExtension)
2647
2648	# define contents of Structure Factor entry
2649	self.Parameters = []
2650	'self.Parameters is a list with two dicts for data parameter settings'
2651	self.InitParameters()
2652	self.RefDict = {'RefList':[],'FF':{},'Super':0}
2653	self.Banks = [] #for multi bank data (usually TOF)
2654	'''self.RefDict is a dict containing the reflection information, as read from the file.
2655	Item 'RefList' contains the reflection information. See the
2656	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
2657	for the contents of each row. Dict element 'FF'
2658	contains the form factor values for each element type; if this entry
2659	is left as initialized (an empty list) it will be initialized as needed later.
2660	'''
2661	def ReInitialize(self):
2662	'Reinitialize the Reader to initial settings'
2663	ImportBaseclass.ReInitialize(self)
2664	self.InitParameters()
2665	self.Banks = [] #for multi bank data (usually TOF)
2666	self.RefDict = {'RefList':[],'FF':{},'Super':0}
2667
2668	def InitParameters(self):
2669	'initialize the instrument parameters structure'
2670	Lambda = 0.70926
2671	HistType = 'SXC'
2672	self.Parameters = [{'Type':[HistType,HistType], # create the structure
2673	'Lam':[Lambda,Lambda]
2674	}, {}]
2675	'Parameters is a list with two dicts for data parameter settings'
2676
2677	def UpdateParameters(self,Type=None,Wave=None):
2678	'Revise the instrument parameters'
2679	if Type is not None:
2680	self.Parameters[0]['Type'] = [Type,Type]
2681	if Wave is not None:
2682	self.Parameters[0]['Lam'] = [Wave,Wave]
2683
2684	######################################################################
2685	class ImportPowderData(ImportBaseclass):
2686	'''Defines a base class for the reading of files with powder data.
2687
2688	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2689	in :meth:`GSASIIdataGUI.GSASII.OnImportPowder` and in
2690	:func:`GSASIIscriptable.import_generic`.
2691	See :ref:`Writing a Import Routine<import_routines>`
2692	for an explanation on how to use this class.
2693	'''
2694	def __init__(self,formatName,longFormatName=None,
2695	extensionlist=[],strictExtension=False,):
2696	ImportBaseclass.__init__(self,formatName,longFormatName,
2697	extensionlist,strictExtension)
2698	self.clockWd = None # used in TOF
2699	self.ReInitialize()
2700
2701	def ReInitialize(self):
2702	'Reinitialize the Reader to initial settings'
2703	ImportBaseclass.ReInitialize(self)
2704	self.powderentry = ['',None,None] # (filename,Pos,Bank)
2705	self.powderdata = [] # Powder dataset
2706	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2707	np.array(x), # x-axis values
2708	np.array(y), # powder pattern intensities
2709	np.array(w), # 1/sig(intensity)^2 values (weights)
2710	np.array(yc), # calc. intensities (zero)
2711	np.array(yb), # calc. background (zero)
2712	np.array(yd), # obs-calc profiles
2713	'''
2714	self.comments = []
2715	self.idstring = ''
2716	self.Sample = SetDefaultSample() # default sample parameters
2717	self.Controls = {} # items to be placed in top-level Controls
2718	self.GSAS = None # used in TOF
2719	self.repeat_instparm = True # Should a parm file be
2720	# used for multiple histograms?
2721	self.instparm = None # name hint from file of instparm to use
2722	self.instfile = '' # full path name to instrument parameter file
2723	self.instbank = '' # inst parm bank number
2724	self.instmsg = '' # a label that gets printed to show
2725	# where instrument parameters are from
2726	self.numbanks = 1
2727	self.instdict = {} # place items here that will be transferred to the instrument parameters
2728	self.pwdparms = {} # place parameters that are transferred directly to the tree
2729	# here (typically from an existing GPX file)
2730	######################################################################
2731	class ImportSmallAngleData(ImportBaseclass):
2732	'''Defines a base class for the reading of files with small angle data.
2733	See :ref:`Writing a Import Routine<import_routines>`
2734	for an explanation on how to use this class.
2735	'''
2736	def __init__(self,formatName,longFormatName=None,extensionlist=[],
2737	strictExtension=False,):
2738
2739	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2740	strictExtension)
2741	self.ReInitialize()
2742
2743	def ReInitialize(self):
2744	'Reinitialize the Reader to initial settings'
2745	ImportBaseclass.ReInitialize(self)
2746	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
2747	self.smallangledata = [] # SASD dataset
2748	'''A small angle data set is a list with items [x,y,w,yc,yd]:
2749	np.array(x), # x-axis values
2750	np.array(y), # powder pattern intensities
2751	np.array(w), # 1/sig(intensity)^2 values (weights)
2752	np.array(yc), # calc. intensities (zero)
2753	np.array(yd), # obs-calc profiles
2754	np.array(yb), # preset bkg
2755	'''
2756	self.comments = []
2757	self.idstring = ''
2758	self.Sample = SetDefaultSample()
2759	self.GSAS = None # used in TOF
2760	self.clockWd = None # used in TOF
2761	self.numbanks = 1
2762	self.instdict = {} # place items here that will be transferred to the instrument parameters
2763
2764	######################################################################
2765	class ImportReflectometryData(ImportBaseclass):
2766	'''Defines a base class for the reading of files with reflectometry data.
2767	See :ref:`Writing a Import Routine<import_routines>`
2768	for an explanation on how to use this class.
2769	'''
2770	def __init__(self,formatName,longFormatName=None,extensionlist=[],
2771	strictExtension=False,):
2772
2773	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2774	strictExtension)
2775	self.ReInitialize()
2776
2777	def ReInitialize(self):
2778	'Reinitialize the Reader to initial settings'
2779	ImportBaseclass.ReInitialize(self)
2780	self.reflectometryentry = ['',None,None] # (filename,Pos,Bank)
2781	self.reflectometrydata = [] # SASD dataset
2782	'''A small angle data set is a list with items [x,y,w,yc,yd]:
2783	np.array(x), # x-axis values
2784	np.array(y), # powder pattern intensities
2785	np.array(w), # 1/sig(intensity)^2 values (weights)
2786	np.array(yc), # calc. intensities (zero)
2787	np.array(yd), # obs-calc profiles
2788	np.array(yb), # preset bkg
2789	'''
2790	self.comments = []
2791	self.idstring = ''
2792	self.Sample = SetDefaultSample()
2793	self.GSAS = None # used in TOF
2794	self.clockWd = None # used in TOF
2795	self.numbanks = 1
2796	self.instdict = {} # place items here that will be transferred to the instrument parameters
2797
2798	######################################################################
2799	class ImportPDFData(ImportBaseclass):
2800	'''Defines a base class for the reading of files with PDF G(R) data.
2801	See :ref:`Writing a Import Routine<import_routines>`
2802	for an explanation on how to use this class.
2803	'''
2804	def __init__(self,formatName,longFormatName=None,extensionlist=[],
2805	strictExtension=False,):
2806
2807	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2808	strictExtension)
2809	self.ReInitialize()
2810
2811	def ReInitialize(self):
2812	'Reinitialize the Reader to initial settings'
2813	ImportBaseclass.ReInitialize(self)
2814	self.pdfentry = ['',None,None] # (filename,Pos,Bank)
2815	self.pdfdata = [] # PDF G(R) dataset
2816	'''A pdf g(r) data set is a list with items [x,y]:
2817	np.array(x), # r-axis values
2818	np.array(y), # pdf g(r)
2819	'''
2820	self.comments = []
2821	self.idstring = ''
2822	self.numbanks = 1
2823
2824	######################################################################
2825	class ImportImage(ImportBaseclass):
2826	'''Defines a base class for the reading of images
2827
2828	Images are read in only these places:
2829
2830	* Initial reading is typically done from a menu item
2831	with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2832	which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2833	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2834	:meth:`Reader`. This returns a list of reader objects for each read image.
2835	Also used in :func:`GSASIIscriptable.import_generic`.
2836
2837	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2838	directly into the data tree.
2839
2840	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
2841
2842	When reading an image, the ``Reader()`` routine in the ImportImage class
2843	should set:
2844
2845	* :attr:`Comments`: a list of strings (str),
2846	* :attr:`Npix`: the number of pixels in the image (int),
2847	* :attr:`Image`: the actual image as a numpy array (np.array)
2848	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2849	data items are needed:
2850
2851	* 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2852	* 'wavelength': wavelength in :math:`\\AA`.
2853	* 'distance': distance of detector from sample in cm.
2854	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2855	* 'size': size of image (such as ``[2048,2048]``).
2856	* 'ImageTag': image number or other keyword used to retrieve image from
2857	a multi-image data file (defaults to ``1`` if not specified).
2858	* 'sumfile': holds sum image file name if a sum was produced from a multi image file
2859
2860	optional data items:
2861
2862	* :attr:`repeat`: set to True if there are additional images to
2863	read in the file, False otherwise
2864	* :attr:`repeatcount`: set to the number of the image.
2865
2866	Note that the above is initialized with :meth:`InitParameters`.
2867	(Also see :ref:`Writing a Import Routine<import_routines>`
2868	for an explanation on how to use import classes in general.)
2869	'''
2870	def __init__(self,formatName,longFormatName=None,extensionlist=[],
2871	strictExtension=False,):
2872	ImportBaseclass.__init__(self,formatName,longFormatName,
2873	extensionlist,strictExtension)
2874	self.InitParameters()
2875
2876	def ReInitialize(self):
2877	'Reinitialize the Reader to initial settings -- not used at present'
2878	ImportBaseclass.ReInitialize(self)
2879	self.InitParameters()
2880
2881	def InitParameters(self):
2882	'initialize the instrument parameters structure'
2883	self.Comments = ['No comments']
2884	self.Data = {'samplechangerpos':0.0,'det2theta':0.0,'Gain map':''}
2885	self.Npix = 0
2886	self.Image = None
2887	self.repeat = False
2888	self.repeatcount = 1
2889	self.sumfile = ''
2890
2891	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2892	'''Optionally, call this after reading in an image to load it into the tree.
2893	This saves time by preventing a reread of the same information.
2894	'''
2895	if ParentFrame:
2896	ParentFrame.ImageZ = self.Image # store the image for plotting
2897	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2898	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
2899
2900	#################################################################################################
2901	# shortcut routines
2902	exp = np.exp
2903	sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2904	cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2905	tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2906	sqrt = sq = lambda x: np.sqrt(x)
2907	pi = lambda: np.pi
2908
2909	def FindFunction(f):
2910	'''Find the object corresponding to function f
2911
2912	:param str f: a function name such as 'numpy.exp'
2913	:returns: (pkgdict,pkgobj) where pkgdict contains a dict
2914	that defines the package location(s) and where pkgobj
2915	defines the object associated with the function.
2916	If the function is not found, pkgobj is None.
2917	'''
2918	df = f.split('.')
2919	pkgdict = {}
2920	# no listed module name, try in current namespace
2921	if len(df) == 1:
2922	try:
2923	fxnobj = eval(f)
2924	return pkgdict,fxnobj
2925	except (AttributeError, NameError):
2926	return None,None
2927
2928	# includes a package, see if package is already imported
2929	pkgnam = '.'.join(df[:-1])
2930	try:
2931	fxnobj = eval(f)
2932	pkgdict[pkgnam] = eval(pkgnam)
2933	return pkgdict,fxnobj
2934	except (AttributeError, NameError):
2935	pass
2936	# package not yet imported, so let's try
2937	if '.' not in sys.path: sys.path.append('.')
2938	pkgnam = '.'.join(df[:-1])
2939	#for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2940	# if pkgname:
2941	# pkgname += '.' + pkg
2942	# else:
2943	# pkgname = pkg
2944	try:
2945	exec('import '+pkgnam)
2946	pkgdict[pkgnam] = eval(pkgnam)
2947	fxnobj = eval(f)
2948	except Exception as msg:
2949	print('load of '+pkgnam+' failed with error='+str(msg))
2950	return {},None
2951	# can we access the function? I am not exactly sure what
2952	# I intended this to test originally (BHT)
2953	try:
2954	fxnobj = eval(f,globals(),pkgdict)
2955	return pkgdict,fxnobj
2956	except Exception as msg:
2957	print('call to',f,' failed with error=',str(msg))
2958	return None,None # not found
2959
2960	class ExpressionObj(object):
2961	'''Defines an object with a user-defined expression, to be used for
2962	secondary fits or restraints. Object is created null, but is changed
2963	using :meth:`LoadExpression`. This contains only the minimum
2964	information that needs to be stored to save and load the expression
2965	and how it is mapped to GSAS-II variables.
2966	'''
2967	def __init__(self):
2968	self.expression = ''
2969	'The expression as a text string'
2970	self.assgnVars = {}
2971	'''A dict where keys are label names in the expression mapping to a GSAS-II
2972	variable. The value a G2 variable name.
2973	Note that the G2 variable name may contain a wild-card and correspond to
2974	multiple values.
2975	'''
2976	self.freeVars = {}
2977	'''A dict where keys are label names in the expression mapping to a free
2978	parameter. The value is a list with:
2979
2980	* a name assigned to the parameter
2981	* a value for to the parameter and
2982	* a flag to determine if the variable is refined.
2983	'''
2984	self.depVar = None
2985
2986	self.lastError = ('','')
2987	'''Shows last encountered error in processing expression
2988	(list of 1-3 str values)'''
2989
2990	self.distance_dict = None # to be used for defining atom phase/symmetry info
2991	self.distance_atoms = None # to be used for defining atom distances
2992
2993	def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2994	'''Load the expression and associated settings into the object. Raises
2995	an exception if the expression is not parsed, if not all functions
2996	are defined or if not all needed parameter labels in the expression
2997	are defined.
2998
2999	This will not test if the variable referenced in these definitions
3000	are actually in the parameter dictionary. This is checked when the
3001	computation for the expression is done in :meth:`SetupCalc`.
3002
3003	:param str expr: the expression
3004	:param list exprVarLst: parameter labels found in the expression
3005	:param dict varSelect: this will be 0 for Free parameters
3006	and non-zero for expression labels linked to G2 variables.
3007	:param dict varName: Defines a name (str) associated with each free parameter
3008	:param dict varValue: Defines a value (float) associated with each free parameter
3009	:param dict varRefflag: Defines a refinement flag (bool)
3010	associated with each free parameter
3011	'''
3012	self.expression = expr
3013	self.compiledExpr = None
3014	self.freeVars = {}
3015	self.assgnVars = {}
3016	for v in exprVarLst:
3017	if varSelect[v] == 0:
3018	self.freeVars[v] = [
3019	varName.get(v),
3020	varValue.get(v),
3021	varRefflag.get(v),
3022	]
3023	else:
3024	self.assgnVars[v] = varName[v]
3025	self.CheckVars()
3026
3027	def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
3028	'''Load the expression and associated settings from the object into
3029	arrays used for editing.
3030
3031	:param list exprVarLst: parameter labels found in the expression
3032	:param dict varSelect: this will be 0 for Free parameters
3033	and non-zero for expression labels linked to G2 variables.
3034	:param dict varName: Defines a name (str) associated with each free parameter
3035	:param dict varValue: Defines a value (float) associated with each free parameter
3036	:param dict varRefflag: Defines a refinement flag (bool)
3037	associated with each free parameter
3038
3039	:returns: the expression as a str
3040	'''
3041	for v in self.freeVars:
3042	varSelect[v] = 0
3043	varName[v] = self.freeVars[v][0]
3044	varValue[v] = self.freeVars[v][1]
3045	varRefflag[v] = self.freeVars[v][2]
3046	for v in self.assgnVars:
3047	varSelect[v] = 1
3048	varName[v] = self.assgnVars[v]
3049	return self.expression
3050
3051	def GetVaried(self):
3052	'Returns the names of the free parameters that will be refined'
3053	return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
3054
3055	def GetVariedVarVal(self):
3056	'Returns the names and values of the free parameters that will be refined'
3057	return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
3058
3059	def UpdateVariedVars(self,varyList,values):
3060	'Updates values for the free parameters (after a refinement); only updates refined vars'
3061	for v in self.freeVars:
3062	if not self.freeVars[v][2]: continue
3063	if "::"+self.freeVars[v][0] not in varyList: continue
3064	indx = list(varyList).index("::"+self.freeVars[v][0])
3065	self.freeVars[v][1] = values[indx]
3066
3067	def GetIndependentVars(self):
3068	'Returns the names of the required independent parameters used in expression'
3069	return [self.assgnVars[v] for v in self.assgnVars]
3070
3071	def CheckVars(self):
3072	'''Check that the expression can be parsed, all functions are
3073	defined and that input loaded into the object is internally
3074	consistent. If not an Exception is raised.
3075
3076	:returns: a dict with references to packages needed to
3077	find functions referenced in the expression.
3078	'''
3079	ret = self.ParseExpression(self.expression)
3080	if not ret:
3081	raise Exception("Expression parse error")
3082	exprLblList,fxnpkgdict = ret
3083	# check each var used in expression is defined
3084	defined = list(self.assgnVars.keys()) + list(self.freeVars.keys())
3085	notfound = []
3086	for var in exprLblList:
3087	if var not in defined:
3088	notfound.append(var)
3089	if notfound:
3090	msg = 'Not all variables defined'
3091	msg1 = 'The following variables were not defined: '
3092	msg2 = ''
3093	for var in notfound:
3094	if msg: msg += ', '
3095	msg += var
3096	self.lastError = (msg1,' '+msg2)
3097	raise Exception(msg)
3098	return fxnpkgdict
3099
3100	def ParseExpression(self,expr):
3101	'''Parse an expression and return a dict of called functions and
3102	the variables used in the expression. Returns None in case an error
3103	is encountered. If packages are referenced in functions, they are loaded
3104	and the functions are looked up into the modules global
3105	workspace.
3106
3107	Note that no changes are made to the object other than
3108	saving an error message, so that this can be used for testing prior
3109	to the save.
3110
3111	:returns: a list of used variables
3112	'''
3113	self.lastError = ('','')
3114	import ast
3115	def ASTtransverse(node,fxn=False):
3116	'''Transverse a AST-parsed expresson, compiling a list of variables
3117	referenced in the expression. This routine is used recursively.
3118
3119	:returns: varlist,fxnlist where
3120	varlist is a list of referenced variable names and
3121	fxnlist is a list of used functions
3122	'''
3123	varlist = []
3124	fxnlist = []
3125	if isinstance(node, list):
3126	for b in node:
3127	v,f = ASTtransverse(b,fxn)
3128	varlist += v
3129	fxnlist += f
3130	elif isinstance(node, ast.AST):
3131	for a, b in ast.iter_fields(node):
3132	if isinstance(b, ast.AST):
3133	if a == 'func':
3134	fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
3135	continue
3136	v,f = ASTtransverse(b,fxn)
3137	varlist += v
3138	fxnlist += f
3139	elif isinstance(b, list):
3140	v,f = ASTtransverse(b,fxn)
3141	varlist += v
3142	fxnlist += f
3143	elif node.__class__.__name__ == "Name":
3144	varlist += [b]
3145	elif fxn and node.__class__.__name__ == "Attribute":
3146	varlist += [b]
3147	return varlist,fxnlist
3148	try:
3149	exprast = ast.parse(expr)
3150	except SyntaxError:
3151	s = ''
3152	import traceback
3153	for i in traceback.format_exc().splitlines()[-3:-1]:
3154	if s: s += "\n"
3155	s += str(i)
3156	self.lastError = ("Error parsing expression:",s)
3157	return
3158	# find the variables & functions
3159	v,f = ASTtransverse(exprast)
3160	varlist = sorted(list(set(v)))
3161	fxnlist = list(set(f))
3162	pkgdict = {}
3163	# check the functions are defined
3164	for fxn in fxnlist:
3165	fxndict,fxnobj = FindFunction(fxn)
3166	if not fxnobj:
3167	self.lastError = ("Error: Invalid function",fxn,
3168	"is not defined")
3169	return
3170	if not hasattr(fxnobj,'__call__'):
3171	self.lastError = ("Error: Not a function.",fxn,
3172	"cannot be called as a function")
3173	return
3174	pkgdict.update(fxndict)
3175	return varlist,pkgdict
3176
3177	def GetDepVar(self):
3178	'return the dependent variable, or None'
3179	return self.depVar
3180
3181	def SetDepVar(self,var):
3182	'Set the dependent variable, if used'
3183	self.depVar = var
3184	#==========================================================================
3185	class ExpressionCalcObj(object):
3186	'''An object used to evaluate an expression from a :class:`ExpressionObj`
3187	object.
3188
3189	:param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
3190	an expression string and mappings for the parameter labels in that object.
3191	'''
3192	def __init__(self,exprObj):
3193	self.eObj = exprObj
3194	'The expression and mappings; a :class:`ExpressionObj` object'
3195	self.compiledExpr = None
3196	'The expression as compiled byte-code'
3197	self.exprDict = {}
3198	'''dict that defines values for labels used in expression and packages
3199	referenced by functions
3200	'''
3201	self.lblLookup = {}
3202	'''Lookup table that specifies the expression label name that is
3203	tied to a particular GSAS-II parameters in the parmDict.
3204	'''
3205	self.fxnpkgdict = {}
3206	'''a dict with references to packages needed to
3207	find functions referenced in the expression.
3208	'''
3209	self.varLookup = {}
3210	'''Lookup table that specifies the GSAS-II variable(s)
3211	indexed by the expression label name. (Used for only for diagnostics
3212	not evaluation of expression.)
3213	'''
3214	self.su = None
3215	'''Standard error evaluation where supplied by the evaluator
3216	'''
3217	# Patch: for old-style expressions with a (now removed step size)
3218	if '2' in platform.python_version_tuple()[0]:
3219	basestr = basestring
3220	else:
3221	basestr = str
3222	for v in self.eObj.assgnVars:
3223	if not isinstance(self.eObj.assgnVars[v], basestr):
3224	self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
3225	self.parmDict = {}
3226	'''A copy of the parameter dictionary, for distance and angle computation
3227	'''
3228
3229	def SetupCalc(self,parmDict):
3230	'''Do all preparations to use the expression for computation.
3231	Adds the free parameter values to the parameter dict (parmDict).
3232	'''
3233	if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3234	return
3235	self.fxnpkgdict = self.eObj.CheckVars()
3236	# all is OK, compile the expression
3237	self.compiledExpr = compile(self.eObj.expression,'','eval')
3238
3239	# look at first value in parmDict to determine its type
3240	parmsInList = True
3241	if '2' in platform.python_version_tuple()[0]:
3242	basestr = basestring
3243	else:
3244	basestr = str
3245	for key in parmDict:
3246	val = parmDict[key]
3247	if isinstance(val, basestr):
3248	parmsInList = False
3249	break
3250	try: # check if values are in lists
3251	val = parmDict[key][0]
3252	except (TypeError,IndexError):
3253	parmsInList = False
3254	break
3255
3256	# set up the dicts needed to speed computations
3257	self.exprDict = {}
3258	self.lblLookup = {}
3259	self.varLookup = {}
3260	for v in self.eObj.freeVars:
3261	varname = self.eObj.freeVars[v][0]
3262	varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
3263	self.lblLookup[varname] = v
3264	self.varLookup[v] = varname
3265	if parmsInList:
3266	parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
3267	else:
3268	parmDict[varname] = self.eObj.freeVars[v][1]
3269	self.exprDict[v] = self.eObj.freeVars[v][1]
3270	for v in self.eObj.assgnVars:
3271	varname = self.eObj.assgnVars[v]
3272	if varname in parmDict:
3273	self.lblLookup[varname] = v
3274	self.varLookup[v] = varname
3275	if parmsInList:
3276	self.exprDict[v] = parmDict[varname][0]
3277	else:
3278	self.exprDict[v] = parmDict[varname]
3279	elif '*' in varname:
3280	varlist = LookupWildCard(varname,list(parmDict.keys()))
3281	if len(varlist) == 0:
3282	raise Exception("No variables match "+str(v))
3283	for var in varlist:
3284	self.lblLookup[var] = v
3285	if parmsInList:
3286	self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
3287	else:
3288	self.exprDict[v] = np.array([parmDict[var] for var in varlist])
3289	self.varLookup[v] = [var for var in varlist]
3290	else:
3291	self.exprDict[v] = None
3292	# raise Exception,"No value for variable "+str(v)
3293	self.exprDict.update(self.fxnpkgdict)
3294
3295	def UpdateVars(self,varList,valList):
3296	'''Update the dict for the expression with a set of values
3297	:param list varList: a list of variable names
3298	:param list valList: a list of corresponding values
3299	'''
3300	for var,val in zip(varList,valList):
3301	self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
3302
3303	def UpdateDict(self,parmDict):
3304	'''Update the dict for the expression with values in a dict
3305	:param dict parmDict: a dict of values, items not in use are ignored
3306	'''
3307	if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3308	self.parmDict = parmDict
3309	return
3310	for var in parmDict:
3311	if var in self.lblLookup:
3312	self.exprDict[self.lblLookup[var]] = parmDict[var]
3313
3314	def EvalExpression(self):
3315	'''Evaluate an expression. Note that the expression
3316	and mapping are taken from the :class:`ExpressionObj` expression object
3317	and the parameter values were specified in :meth:`SetupCalc`.
3318	:returns: a single value for the expression. If parameter
3319	values are arrays (for example, from wild-carded variable names),
3320	the sum of the resulting expression is returned.
3321
3322	For example, if the expression is ``'A*B'``,
3323	where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
3324
3325	[0.5, 1, 0.5]
3326
3327	then the result will be ``4.0``.
3328	'''
3329	self.su = None
3330	if self.eObj.expression.startswith('Dist'):
3331	# GSASIIpath.IPyBreak()
3332	dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
3333	return dist
3334	elif self.eObj.expression.startswith('Angle'):
3335	angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
3336	return angle
3337	if self.compiledExpr is None:
3338	raise Exception("EvalExpression called before SetupCalc")
3339	try:
3340	val = eval(self.compiledExpr,globals(),self.exprDict)
3341	except TypeError:
3342	val = None
3343	if not np.isscalar(val):
3344	val = np.sum(val)
3345	return val
3346
3347	class G2Exception(Exception):
3348	'A generic GSAS-II exception class'
3349	def __init__(self,msg):
3350	self.msg = msg
3351	def __str__(self):
3352	return repr(self.msg)
3353
3354	class G2RefineCancel(Exception):
3355	'Raised when Cancel is pressed in a refinement dialog'
3356	def __init__(self,msg):
3357	self.msg = msg
3358	def __str__(self):
3359	return repr(self.msg)
3360
3361	def HowDidIgetHere(wherecalledonly=False):
3362	'''Show a traceback with calls that brought us to the current location.
3363	Used for debugging.
3364	'''
3365	import traceback
3366	if wherecalledonly:
3367	i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
3368	print(i.strip().rstrip())
3369	else:
3370	print (70'')
3371	for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
3372	print (70'')
3373
3374	# Note that this is GUI code and should be moved at somepoint
3375	def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
3376	'''Create and initialize a new set of PDF tree entries
3377
3378	:param Frame G2frame: main GSAS-II tree frame object
3379	:param str PWDRtree: name of PWDR to be used to create PDF item
3380	:param dict ElList: data structure with composition
3381	:param list Qlimits: Q limits to be used for computing the PDF
3382	:param float numAtm: no. atom in chemical formula
3383	:param float FltBkg: flat background value
3384	:param list PDFnames: previously used PDF names
3385
3386	:returns: the Id of the newly created PDF entry
3387	'''
3388	PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
3389	if PDFname in PDFnames:
3390	print('Skipping, entry already exists: '+PDFname)
3391	return None
3392	#PDFname = MakeUniqueLabel(PDFname,PDFnames)
3393	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
3394	Data = {
3395	'Sample':{'Name':PWDRtree,'Mult':1.0},
3396	'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
3397	'Container':{'Name':'','Mult':-1.0,'Refine':False},
3398	'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
3399	'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
3400	'DetType':'Area detector','ObliqCoeff':0.3,'Ruland':0.025,'QScaleLim':Qlimits,
3401	'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,'Rmin':1.0,
3402	'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[],
3403	#items for sequential PDFfit
3404	'Datarange':[0.,30.],'Fitrange':[0.,30.],'qdamp':[0.03,False],'qbroad':[0,False],'Temp':300}
3405	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
3406	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
3407	{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
3408	return Id
3409
3410	class ShowTiming(object):
3411	'''An object to use for timing repeated sections of code.
3412
3413	Create the object with::
3414	tim0 = ShowTiming()
3415
3416	Tag sections of code to be timed with::
3417	tim0.start('start')
3418	tim0.start('in section 1')
3419	tim0.start('in section 2')
3420
3421	etc. (Note that each section should have a unique label.)
3422
3423	After the last section, end timing with::
3424	tim0.end()
3425
3426	Show timing results with::
3427	tim0.show()
3428
3429	'''
3430	def __init__(self):
3431	self.timeSum = []
3432	self.timeStart = []
3433	self.label = []
3434	self.prev = None
3435	def start(self,label):
3436	import time
3437	if label in self.label:
3438	i = self.label.index(label)
3439	self.timeStart[i] = time.time()
3440	else:
3441	i = len(self.label)
3442	self.timeSum.append(0.0)
3443	self.timeStart.append(time.time())
3444	self.label.append(label)
3445	if self.prev is not None:
3446	self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
3447	self.prev = i
3448	def end(self):
3449	import time
3450	if self.prev is not None:
3451	self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
3452	self.prev = None
3453	def show(self):
3454	sumT = sum(self.timeSum)
3455	print('Timing results (total={:.2f} sec)'.format(sumT))
3456	for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
3457	print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.val,100val/sumT))
3458
3459	def validateAtomDrawType(typ,generalData={}):
3460	'''Confirm that the selected Atom drawing type is valid for the current
3461	phase. If not, use 'vdW balls'. This is currently used only for setting a
3462	default when atoms are added to the atoms draw list.
3463	'''
3464	if typ in ('lines','vdW balls','sticks','balls & sticks','ellipsoids'):
3465	return typ
3466	# elif generalData.get('Type','') == 'macromolecular':
3467	# if typ in ('backbone',):
3468	# return typ
3469	return 'vdW balls'
3470
3471	if __name__ == "__main__":
3472	# test variable descriptions
3473	for var in '0::Afrac:*',':1:Scale','1::dAx:0','::undefined':
3474	v = var.split(':')[2]
3475	print(var+':\t', getDescr(v),getVarStep(v))
3476	import sys; sys.exit()
3477	# test equation evaluation
3478	def showEQ(calcobj):
3479	print (50*'=')
3480	print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
3481	for v in sorted(calcobj.varLookup):
3482	print (" "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
3483	# print ' Derivatives'
3484	# for v in calcobj.derivStep.keys():
3485	# print ' d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
3486
3487	obj = ExpressionObj()
3488
3489	obj.expression = "A*np.exp(B)"
3490	obj.assgnVars = {'B': '0::Afrac:1'}
3491	obj.freeVars = {'A': [u'A', 0.5, True]}
3492	#obj.CheckVars()
3493	calcobj = ExpressionCalcObj(obj)
3494
3495	obj1 = ExpressionObj()
3496	obj1.expression = "A*np.exp(B)"
3497	obj1.assgnVars = {'B': '0::Afrac:*'}
3498	obj1.freeVars = {'A': [u'Free Prm A', 0.5, True]}
3499	#obj.CheckVars()
3500	calcobj1 = ExpressionCalcObj(obj1)
3501
3502	obj2 = ExpressionObj()
3503	obj2.distance_stuff = np.array([[0,1],[1,-1]])
3504	obj2.expression = "Dist(1,2)"
3505	GSASIIpath.InvokeDebugOpts()
3506	parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3507	calcobj2 = ExpressionCalcObj(obj2)
3508	calcobj2.SetupCalc(parmDict2)
3509	showEQ(calcobj2)
3510
3511	parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
3512	print ('\nDict = '+parmDict1)
3513	calcobj.SetupCalc(parmDict1)
3514	showEQ(calcobj)
3515	calcobj1.SetupCalc(parmDict1)
3516	showEQ(calcobj1)
3517
3518	parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3519	print ('Dict = '+parmDict2)
3520	calcobj.SetupCalc(parmDict2)
3521	showEQ(calcobj)
3522	calcobj1.SetupCalc(parmDict2)
3523	showEQ(calcobj1)
3524	calcobj2.SetupCalc(parmDict2)
3525	showEQ(calcobj2)

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