source: trunk/GSASIIobj.py @ 4824

Last change on this file since 4824 was 4824, checked in by vondreele, 9 months ago

add new refinable RB parameter for atom site fraction - always there; can be used in constraints.. Available for residue & vector style RBs
fixes to delete RB routines
fixes to RB naming when adding RB to structure
Implement use of view position for new RB origin

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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2021-02-20 20:44:46 +0000 (Sat, 20 Feb 2021) $
5# $Author: vondreele $
6# $Revision: 4824 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 4824 2021-02-20 20:44:46Z vondreele $
9########### SVN repository information ###################
10
11'''
12*GSASIIobj: Data objects*
13=========================
14
15This module defines and/or documents the data structures used in GSAS-II, as well
16as 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
30Constraints Tree Item
31----------------------
32
33Constraints are stored in a dict, separated into groups.
34Note that parameter are named in the following pattern,
35p: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.
37If a parameter does not depend on a histogram or phase or is unnumbered, that
38number is omitted.
39Note that the contents of each dict item is a List where each element in the
40list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
41The constraints in this form are converted in
42:func:`GSASIIstrIO.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
43
44The keys in the Constraints dict are:
45
46.. tabularcolumns:: |l|p{4.5in}|
47
48==========  ====================================================
49  key         explanation
50==========  ====================================================
51Hist        This specifies a list of constraints on
52            histogram-related parameters,
53            which will be of form :h:<var>:n.
54HAP         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.
57Phase       This specifies a list of constraints on phase
58            parameters,
59            which will be of form p::<var>:n.
60Global      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
71Each constraint is defined as an item in a list. Each constraint is of form::
72
73[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
74
75Where 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 (previously a str variable name of form
79      'p:h:name[:at]')
80
81Note that the last three items in the list play a special role:
82
83 * <fixedval> is the fixed value for a `constant equation` (``constype=c``)
84   constraint or is None. For a `New variable` (``constype=f``) constraint,
85   a variable name can be specified as a str (used for externally
86   generated constraints)
87 * <varyflag> is True or False for `New variable` (``constype=f``) constraints
88   or is None. This indicates if this variable should be refined.
89 * <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
90
91    * 'e' defines a set of equivalent variables. Only the first variable is refined (if the
92      appropriate refine flag is set) and and all other equivalent variables in the list
93      are generated from that variable, using the appropriate multipliers.
94    * 'c' defines a constraint equation of form,
95      :math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
96    * 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
97      even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
98      constraint and the mult value is ignored.
99      This is of particular value when needing to hold one or more variables where a
100      single flag controls a set of variables such as, coordinates,
101      the reciprocal metric tensor or anisotropic displacement parameter.
102    * 'f' defines a new variable (function) according to relationship
103      :math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
104
105.. _Covariance_table:
106
107.. index::
108   single: Covariance description
109   single: Data object descriptions; Covariance
110
111Covariance Tree Item
112--------------------
113
114The Covariance tree item has results from the last least-squares run. They
115are stored in a dict with these keys:
116
117.. tabularcolumns:: |l|l|p{4in}|
118
119=============  ===============  ====================================================
120  key            sub-key        explanation
121=============  ===============  ====================================================
122newCellDict    \\                (dict) ith lattice parameters computed by
123                                :func:`GSASIIstrMath.GetNewCellParms`
124title          \\                (str) Name of gpx file(?)
125variables      \\                (list) Values for all N refined variables
126                                (list of float values, length N,
127                                ordered to match varyList)
128sig            \\                (list) Uncertainty values for all N refined variables
129                                (list of float values, length N,
130                                ordered to match varyList)
131varyList       \\                (list of str values, length N) List of directly refined variables
132                               
133newAtomDict    \\                (dict) atom position values computed in
134                                :func:`GSASIIstrMath.ApplyXYZshifts`
135Rvals          \\                (dict) R-factors, GOF, Marquardt value for last
136                                refinement cycle
137\\              Nobs             (int) Number of observed data points
138\\              Rwp              (float) overall weighted profile R-factor (%)
139\\              chisq            (float) :math:`\\sum w*(I_{obs}-I_{calc})^2`                               
140                                for all data.
141                                Note: this is not the reduced :math:`\\chi^2`.
142\\              lamMax           (float) Marquardt value applied to Hessian diagonal
143\\              GOF              (float) The goodness-of-fit, aka square root of
144                                the reduced chi squared.
145covMatrix      \\                (np.array) The (NxN) covVariance matrix
146=============  ===============  ====================================================
147
148.. _Phase_table:
149
150.. index::
151   single: Phase object description
152   single: Data object descriptions; Phase
153
154Phase Tree Items
155----------------
156
157Phase information is stored in the GSAS-II data tree as children of the
158Phases item in a dict with keys:
159
160.. tabularcolumns:: |l|l|p{4in}|
161
162==========  ===============     =====================================================================================================
163  key         sub-key           explanation
164==========  ===============     =====================================================================================================
165General         \\               (dict) Overall information for the phase
166  \\         3Dproj              (list of str) projections for 3D pole distribution plots
167  \\         AngleRadii          (list of floats) Default radius for each atom used to compute
168                                interatomic angles
169  \\         AtomMass            (list of floats) Masses for atoms
170  \\         AtomPtrs            (list of int) four locations (cx,ct,cs & cu) to use to pull info
171                                from the atom records
172  \\         AtomTypes           (llist of str) Atom types
173  \\         BondRadii           (list of floats) Default radius for each atom used to compute
174                                interatomic distances
175  \\         Cell                Unit cell parameters & ref. flag
176                                (list with 8 items. All but first item are float.)
177
178                                 0: cell refinement flag (True/False),
179                                 1-3: a, b, c, (:math:`\\AA`)
180                                 4-6: alpha, beta & gamma, (degrees)
181                                 7: volume (:math:`\\AA^3`)
182  \\         Color               (list of (r,b,g) triplets) Colors for atoms
183  \\         Compare             (dict) Polygon comparison parameters
184  \\         Data plot type      (str) data plot type ('Mustrain', 'Size' or
185                                'Preferred orientation') for powder data
186  \\         DisAglCtls          (dDict) with distance/angle search controls,
187                                which has keys 'Name', 'AtomTypes',
188                                'BondRadii', 'AngleRadii' which are as above
189                                except are possibly edited. Also contains
190                                'Factors', which is a 2 element list with
191                                a multiplier for bond and angle search range
192                                [typically (0.85,0.85)].
193  \\         F000X               (float) x-ray F(000) intensity
194  \\         F000N               (float) neutron F(000) intensity
195  \\         Flip                (dict) Charge flip controls
196  \\         HydIds              (dict) geometrically generated hydrogen atoms
197  \\         Isotope             (dict) Isotopes for each atom type
198  \\         Isotopes            (dict) Scattering lengths for each isotope
199                                combination for each element in phase
200  \\         MCSA controls       (dict) Monte Carlo-Simulated Annealing controls
201  \\         Map                 (dict) Map parameters
202  \\         Mass                (float) Mass of unit cell contents in g/mol
203  \\         Modulated           (bool) True if phase modulated
204  \\         Mydir               (str) Directory of current .gpx file
205  \\         Name                (str) Phase name
206  \\         NoAtoms             (dict) Number of atoms per unit cell of each type
207  \\         POhkl               (list) March-Dollase preferred orientation direction
208  \\         Pawley dmin         (float) maximum Q (as d-space) to use for Pawley extraction
209  \\         Pawley dmax         (float) minimum Q (as d-space) to use for Pawley extraction
210  \\         Pawley neg wt       (float) Restraint value for negative Pawley intensities
211  \\         SGData              (object) Space group details as a
212                                :ref:`space group (SGData) <SGData_table>`
213                                object, as defined in :func:`GSASIIspc.SpcGroup`.
214  \\         SH Texture          (dict) Spherical harmonic preferred orientation parameters
215  \\         Super               (int) dimension of super group (0,1 only)
216  \\         Type                (str) phase type (e.g. 'nuclear')
217  \\         Z                   (dict) Atomic numbers for each atom type
218  \\         doDysnomia          (bool) flag for max ent map modification via Dysnomia
219  \\         doPawley            (bool) Flag for Pawley intensity extraction
220  \\         vdWRadii            (dict) Van der Waals radii for each atom type
221ranId           \\               (int) unique random number Id for phase
222pId             \\               (int) Phase Id number for current project.
223Atoms           \\               (list of lists) Atoms in phase as a list of lists. The outer list
224                                is for each atom, the inner list contains varying
225                                items depending on the type of phase, see
226                                the :ref:`Atom Records <Atoms_table>` description.
227Drawing         \\               (dict) Display parameters
228\\           Atoms               (list of lists) with an entry for each atom that is drawn
229\\           Plane               (list) Controls for contour density plane display
230\\           Quaternion          (4 element np.array) Viewing quaternion
231\\           Zclip               (float) clipping distance in :math:`\\AA`
232\\           Zstep               (float) Step to de/increase Z-clip
233\\           atomPtrs            (list) positions of x, type, site sym, ADP flag in Draw Atoms
234\\           backColor           (list) background for plot as and R,G,B triplet
235                                (default = [0, 0, 0], black).
236\\           ballScale           (float) Radius of spheres in ball-and-stick display
237\\           bondList            (dict) Bonds
238\\           bondRadius          (float) Radius of binds in :math:`\\AA`
239\\           cameraPos           (float) Viewing position in :math:`\\AA` for plot
240\\           contourLevel        (float) map contour level in :math:`e/\\AA^3`
241\\           contourMax          (float) map contour maximum
242\\           depthFog            (bool) True if use depthFog on plot - set currently as False
243\\           ellipseProb         (float) Probability limit for display of thermal
244                                ellipsoids in % .
245\\           magMult             (float) multiplier for magnetic moment arrows
246\\           mapSize             (float) x & y dimensions of contourmap (fixed internally)
247\\           modelView           (4,4 array) from openGL drawing transofmation matrix
248\\           oldxy               (list with two floats) previous view point
249\\           radiusFactor        (float) Distance ratio for searching for bonds. Bonds
250                                are located that are within r(Ra+Rb) and (Ra+Rb)/r
251                                where Ra and Rb are the atomic radii.
252\\           selectedAtoms       (list of int values) List of selected atoms
253\\           showABC             (bool) Flag to show view point triplet. True=show.
254\\           showHydrogen        (bool) Flag to control plotting of H atoms.
255\\           showRigidBodies     (bool) Flag to highlight rigid body placement
256\\           showSlice           (bool) flag to show contour map
257\\           sizeH               (float) Size ratio for H atoms
258\\           unitCellBox         (bool) Flag to control display of the unit cell.
259\\           vdwScale            (float) Multiplier of van der Waals radius for display of vdW spheres.
260\\           viewDir             (np.array with three floats) cartesian viewing direction
261\\           viewPoint           (list of lists) First item in list is [x,y,z]
262                                in fractional coordinates for the center of
263                                the plot. Second item list of previous & current
264                                atom number viewed (may be [0,0])
265RBModels        \\               Rigid body assignments (note Rigid body definitions
266                                are stored in their own main top-level tree entry.)
267RMC             \\               (dict) RMCProfile & rmcfull controls
268Pawley ref      \\               (list) Pawley reflections
269Histograms      \\               (dict of dicts) The key for the outer dict is
270                                the histograms tied to this phase. The inner
271                                dict contains the combined phase/histogram
272                                parameters for items such as scale factors,
273                                size and strain parameters. The following are the
274                                keys to the inner dict. (dict)
275\\           Babinet             (dict) For protein crystallography. Dictionary with two
276                                entries, 'BabA', 'BabU'
277\\           Extinction          (list of float, bool) Extinction parameter
278\\           Flack               (list of [float, bool]) Flack parameter & refine flag
279\\           HStrain             (list of two lists) Hydrostatic strain. The first is
280                                a list of the HStrain parameters (1, 2, 3, 4, or 6
281                                depending on unit cell), the second is a list of boolean
282                                refinement parameters (same length)
283\\           Histogram           (str) The name of the associated histogram
284\\           Layer Disp          (list of [float, bool]) Layer displacement in beam direction & refine flag
285\\           LeBail              (bool) Flag for LeBail extraction
286\\           Mustrain            (list) Microstrain parameters, in order:
287   
288                                0. Type, one of  u'isotropic', u'uniaxial', u'generalized'
289                                1. Isotropic/uniaxial parameters - list of 3 floats
290                                2. Refinement flags - list of 3 bools
291                                3. Microstrain axis - list of 3 ints, [h, k, l]
292                                4. Generalized mustrain parameters - list of 2-6 floats, depending on space group
293                                5. Generalized refinement flags - list of bools, corresponding to the parameters of (4)
294\\           Pref.Ori.           (list) Preferred Orientation. List of eight parameters.
295                                Items marked SH are only used for Spherical Harmonics.
296                               
297                                0. (str) Type, 'MD' for March-Dollase or 'SH' for Spherical Harmonics
298                                1. (float) Value
299                                2. (bool) Refinement flag
300                                3. (list) Preferred direction, list of ints, [h, k, l]
301                                4. (int) SH - number of terms
302                                5. (dict) SH - 
303                                6. (list) SH
304                                7. (float) SH
305\\           Scale               (list of [float, bool]) Phase fraction & refine flag
306\\           Size                List of crystallite size parameters, in order:
307
308                                0. (str) Type, one of  u'isotropic', u'uniaxial', u'ellipsoidal'
309                                1. (list) Isotropic/uniaxial parameters - list of 3 floats
310                                2. (list) Refinement flags - list of 3 bools
311                                3. (list) Size axis - list of 3 ints, [h, k, l]
312                                4. (list) Ellipsoidal size parameters - list of 6 floats
313                                5. (list) Ellipsoidal refinement flags - list of bools, corresponding to the parameters of (4)
314\\           Use                 (bool) True if this histogram is to be used in refinement
315\\           newLeBail           (bool) Whether to perform a new LeBail extraction
316MCSA            \\               (dict) Monte-Carlo simulated annealing parameters
317==========  ===============     =====================================================================================================
318
319.. _RBData_table:
320
321.. index::
322   single: Rigid Body Data description
323   single: Data object descriptions; Rigid Body Data
324
325Rigid Body Objects
326------------------
327
328Rigid body descriptions are available for two types of rigid bodies: 'Vector'
329and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
330with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
331with defined refinable torsion angles.
332
333.. tabularcolumns:: |l|l|p{4in}|
334
335==========  ===============     ====================================================
336  key         sub-key           explanation
337==========  ===============     ====================================================
338Vector      RBId                (dict of dict) vector rigid bodies
339\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
340\\           RBname              (str) Name assigned by user to rigid body
341\\           VectMag             (list) vector magnitudes in :math:`\\AA`
342\\           rbXYZ               (list of 3 float Cartesian coordinates for Vector rigid body )
343\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
344                                definition, use center of atoms flag
345\\           VectRef             (list of bool refinement flags for VectMag values )
346\\           rbTypes             (list of str) Atom types for each atom in rigid body
347\\           rbVect              (list of lists) Cartesian vectors for each translation used to build rigid body
348\\           useCount            (int) Number of times rigid body is used in any structure
349Residue     RBId                (dict of dict) residue rigid bodies
350\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
351\\           RBname              (str) Name assigned by user to rigid body
352\\           rbXYZ               (list of 3 float) Cartesian coordinates for Residue rigid body
353\\           rbTypes             (list of str) Atom types for each atom in rigid body
354\\           atNames             (list of str) Names of each atom in rigid body (e.g. C1,N2...)
355\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
356                                definition, use center of atoms flag
357\\           rbSeq               (list) Orig,Piv,angle,Riding : definition of internal rigid body
358                                torsion; origin atom (int), pivot atom (int), torsion angle (float),
359                                riding atoms (list of int)
360\\           SelSeq              (int,int) used by SeqSizer to identify objects
361\\           useCount            (int)Number of times rigid body is used in any structure
362RBIds           \\               (dict) unique Ids generated upon creation of each rigid body
363\\           Vector              (list) Ids for each Vector rigid body
364\\           Residue             (list) Ids for each Residue rigid body
365==========  ===============     ====================================================
366
367.. _SGData_table:
368
369.. index::
370   single: Space Group Data description
371   single: Data object descriptions; Space Group Data
372
373Space Group Objects
374-------------------
375
376Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
377and the information is placed in a SGdata object
378which is a dict with these keys. Magnetic ones are marked "mag"
379
380.. tabularcolumns:: |l|p{4.5in}|
381
382==========  ========================================================================================
383  key         explanation
384==========  ========================================================================================
385BNSlattsym  mag - (str) BNS magnetic space group symbol and centering vector
386GenFlg      mag - (list) symmetry generators indices
387GenSym      mag - (list) names for each generator
388MagMom      mag - (list) "time reversals" for each magnetic operator
389MagPtGp     mag - (str) Magnetic point group symbol
390MagSpGrp    mag - (str) Magnetic space group symbol
391OprNames    mag - (list) names for each space group operation
392SGCen       (np.array) Symmetry cell centering vectors. A (n,3) np.array
393            of centers. Will always have at least one row: ``np.array([[0, 0, 0]])``
394SGFixed     (bool) Only True if phase mported from a magnetic cif file
395            then the space group can not be changed by the user because
396            operator set from cif may be nonstandard
397SGGen       (list) generators
398SGGray      (bool) True if space group is a gray group (incommensurate magnetic structures)
399SGInv       (bool) True if centrosymmetric, False if not
400SGLatt      (str)Lattice centering type. Will be one of
401            P, A, B, C, I, F, R
402SGLaue      (str) one of the following 14 Laue classes:
403            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
404            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m
405SGOps       (list) symmetry operations as a list of form
406            ``[[M1,T1], [M2,T2],...]``
407            where :math:`M_n` is a 3x3 np.array
408            and :math:`T_n` is a length 3 np.array.
409            Atom coordinates are transformed where the
410            Asymmetric unit coordinates [X is (x,y,z)]
411            are transformed using
412            :math:`X^\\prime = M_n*X+T_n`
413SGPolax     (str) Axes for space group polarity. Will be one of
414            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
415            'xyz'. In the case where axes are arbitrary
416            '111' is used (P 1, and ?).
417SGPtGrp     (str) Point group of the space group
418SGUniq      unique axis if monoclinic. Will be
419            a, b, or c for monoclinic space groups.
420            Will be blank for non-monoclinic.
421SGSpin      mag - (list) of spin flip operatiors (+1 or -1) for the space group operations
422SGSys       (str) symmetry unit cell: type one of
423            'triclinic', 'monoclinic', 'orthorhombic',
424            'tetragonal', 'rhombohedral', 'trigonal',
425            'hexagonal', 'cubic'
426SSGK1       (list) Superspace multipliers
427SpGrp       (str) space group symbol
428SpnFlp      mag - (list) Magnetic spin flips for every magnetic space group operator
429==========  ========================================================================================
430
431.. _SSGData_table:
432
433.. index::
434   single: Superspace Group Data description
435   single: Data object descriptions; Superspace Group Data
436
437Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
438and the information is placed in a SSGdata object
439which is a dict with these keys:
440
441.. tabularcolumns:: |l|p{4.5in}|
442
443==========  ====================================================
444  key         explanation
445==========  ====================================================
446SSGCen      (list) 4D cell centering vectors [0,0,0,0] at least
447SSGK1       (list) Superspace multipliers
448SSGOps      (list) 4D symmetry operations as [M,T] so that M*x+T = x'
449SSpGrp      (str) superspace group symbol extension to space group
450            symbol, accidental spaces removed
451modQ        (list) modulation/propagation vector
452modSymb     (list of str) Modulation symbols
453==========  ====================================================
454
455
456Phase Information
457--------------------
458
459.. index::
460   single: Phase information record description
461
462Phase information is placed in one of the following keys:
463
464.. tabularcolumns:: |l|p{4.5in}|
465
466==========  ==============================================================
467  key         explanation
468==========  ==============================================================
469General       Overall information about a phase
470Histograms    Information about each histogram linked to the
471              current phase as well as parameters that
472              are defined for each histogram and phase
473              (such as sample peak widths and preferred
474              orientation parameters.
475Atoms         Contains a list of atoms, as described in the
476              :ref:`Atom Records <Atoms_table>` description.
477Drawing       Parameters that determine how the phase is
478              displayed, including a list of atoms to be
479              included, as described in the
480              :ref:`Drawing Atom Records <Drawing_atoms_table>`
481              description
482MCSA          Monte-Carlo simulated annealing parameters
483pId           The index of each phase in the project, numbered
484              starting at 0
485ranId         An int value with a unique value for each phase
486RBModels      A list of dicts with parameters for each
487              rigid body inserted into the current phase,
488              as defined in the
489              :ref:`Rigid Body Insertions <Rigid_Body_Insertions>`.
490              Note that the rigid bodies are defined as
491              :ref:`Rigid Body Objects <RBData_table>`
492RMC           PDF modeling parameters
493Pawley ref    Pawley refinement parameters
494
495==========  ==============================================================
496
497.. _Atoms_table:
498
499.. index::
500   single: Atoms record description
501   single: Data object descriptions; Atoms record
502
503--------------------
504Atom Records
505--------------------
506
507If ``phasedict`` points to the phase information in the data tree, then
508atoms are contained in a list of atom records (list) in
509``phasedict['Atoms']``. Also needed to read atom information
510are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
511which define locations in the atom record, as shown below. Items shown are
512always present; additional ones for macromolecular phases are marked 'mm',
513and those for magnetic structures are marked 'mg'
514
515.. tabularcolumns:: |l|p{4.5in}|
516
517==============      ====================================================
518location            explanation
519==============      ====================================================
520ct-4                mm - (str) residue number
521ct-3                mm - (str) residue name (e.g. ALA)
522ct-2                mm - (str) chain label
523ct-1                (str) atom label
524ct                  (str) atom type
525ct+1                (str) refinement flags; combination of 'F', 'X', 'U', 'M'
526cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
527cx+3                (float) site occupancy
528cx+4,cx+5,cx+6      mg - (list) atom magnetic moment along a,b,c in Bohr magnetons
529cs                  (str) site symmetry
530cs+1                (int) site multiplicity
531cia                 (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
532cia+1               (float) Uiso
533cia+2...cia+7       (6 floats) U11, U22, U33, U12, U13, U23
534atom[cia+8]         (int) unique atom identifier
535
536==============      ====================================================
537
538.. _Drawing_atoms_table:
539
540.. index::
541   single: Drawing atoms record description
542   single: Data object descriptions; Drawing atoms record
543
544----------------------------
545Drawing Atom Records
546----------------------------
547
548If ``phasedict`` points to the phase information in the data tree, then
549drawing atoms are contained in a list of drawing atom records (list) in
550``phasedict['Drawing']['Atoms']``. Also needed to read atom information
551are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
552which define locations in the atom record, as shown below. Items shown are
553always present; additional ones for macromolecular phases are marked 'mm',
554and those for magnetic structures are marked 'mg'
555
556.. tabularcolumns:: |l|p{4.5in}|
557
558==============   ===================================================================================
559location            explanation
560==============   ===================================================================================
561ct-4                mm - (str) residue number
562ct-3                mm - (str) residue name (e.g. ALA)
563ct-2                mm - (str) chain label
564ct-1                (str) atom label
565ct                  (str) atom type
566cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
567cx+3,cx+4,cx+5      mg - (3 floats) atom magnetic moment along a,b,c in Bohr magnetons
568cs-1                (str) Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1')
569cs                  (str) atom drawing style; e.g. 'balls & sticks'
570cs+1                (str) atom label style (e.g. 'name')
571cs+2                (int) atom color (RBG triplet)
572cs+3                (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
573cs+4                (float) Uiso
574cs+5...cs+11        (6 floats) U11, U22, U33, U12, U13, U23
575ci                  (int) unique atom identifier; matches source atom Id in Atom Records
576==============   ===================================================================================
577
578.. _Rigid_Body_Insertions:
579
580----------------------------
581Rigid Body Insertions
582----------------------------
583
584If ``phasedict`` points to the phase information in the data tree, then
585rigid body information is contained in list(s) in
586``phasedict['RBModels']['Residue']`` and/or ``phasedict['RBModels']['Vector']``
587for each rigid body inserted into the current phase.
588
589.. tabularcolumns:: |l|p{4.5in}|
590
591==============   ===================================================================================
592key              explanation
593==============   ===================================================================================
594fixOrig           Should the origin be fixed (when editing, not the refinement flag)
595Ids               Ids for assignment of atoms in the rigid body
596numChain          Chain number for macromolecular fits
597Orient            Orientation of the RB as a quaternion and a refinement flag (' ', 'A' or 'AV')
598OrientVec         Orientation of the RB expressed as a vector and azimuthal rotation angle
599Orig              Origin of the RB in fractional coordinates and refinement flag (bool)
600RBId              References the unique ID of a rigid body in the
601                  :ref:`Rigid Body Objects <RBData_table>`
602RBname            The name for the rigid body (str)
603AtomFrac          The atom fractions for the rigid body
604ThermalMotion     The thermal motion description for the rigid body, which includes a choice for
605                  the model and can include TLS parameters or an overall Uiso value.
606Torsions          Defines the torsion angle and refinement flag for each torsion defined in
607                  the :ref:`Rigid Body Object <RBData_table>`
608==============   ===================================================================================
609
610.. _Powder_table:
611
612.. index::
613   single: Powder data object description
614   single: Data object descriptions; Powder Data
615
616Powder Diffraction Tree Items
617-----------------------------
618
619Every powder diffraction histogram is stored in the GSAS-II data tree
620with a top-level entry named beginning with the string "PWDR ". The
621diffraction data for that information are directly associated with
622that tree item and there are a series of children to that item. The
623routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
624and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
625load this information into a dictionary where the child tree name is
626used as a key, and the information in the main entry is assigned
627a key of ``Data``, as outlined below.
628
629.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
630
631======================     ===============  ===========================================================
632  key                       sub-key          explanation
633======================     ===============  ===========================================================
634Comments                    \\               (list of str) Text strings extracted from the original powder
635                                            data header. These cannot be changed by the user;
636                                            it may be empty.
637Limits                      \\               (list) two two element lists, as [[Ld,Hd],[L,H]]
638                                            where L and Ld are the current and default lowest
639                                            two-theta value to be used and
640                                            where H and Hd are the current and default highest
641                                            two-theta value to be used.
642Reflection Lists            \\               (dict of dicts) with an entry for each phase in the
643                                            histogram. The contents of each dict item
644                                            is a dict containing reflections, as described in
645                                            the :ref:`Powder Reflections <PowderRefl_table>`
646                                            description.
647Instrument Parameters       \\               (dict) The instrument parameters uses different dicts
648                                            for the constant wavelength (CW) and time-of-flight (TOF)
649                                            cases. See below for the descriptions of each.
650wtFactor                    \\               (float) A weighting factor to increase or decrease
651                                            the leverage of data in the histogram .
652                                            A value of 1.0 weights the data with their
653                                            standard uncertainties and a larger value
654                                            increases the weighting of the data (equivalent
655                                            to decreasing the uncertainties).
656Sample Parameters           \\               (dict) Parameters that describe how
657                                            the data were collected, as listed
658                                            below. Refinable parameters are a list containing
659                                            a float and a bool, where the second value
660                                            specifies if the value is refined, otherwise
661                                            the value is a float unless otherwise noted.
662\\                           Scale           The histogram scale factor (refinable)
663\\                           Absorption      The sample absorption coefficient as
664                                            :math:`\\mu r` where r is the radius
665                                            (refinable). Only valid for Debye-Scherrer geometry.
666\\                           SurfaceRoughA   Surface roughness parameter A as defined by
667                                            Surotti, *J. Appl. Cryst*, **5**, 325-331, 1972.
668                                            (refinable - only valid for Bragg-Brentano geometry)
669\\                           SurfaceRoughB   Surface roughness parameter B (refinable -
670                                            only valid for Bragg-Brentano geometry)
671\\                           DisplaceX,      Sample displacement from goniometer center
672                            DisplaceY       where Y is along the beam direction and
673                                            X is perpendicular. Units are :math:`\\mu m`
674                                            (refinable).
675\\                           Phi, Chi,       Goniometer sample setting angles, in degrees.
676                            Omega
677\\                           Gonio. radius   Radius of the diffractometer in mm
678\\                           InstrName       (str) A name for the instrument, used in preparing
679                                            a CIF .
680\\                           Force,          Variables that describe how the measurement
681                            Temperature,    was performed. Not used directly in
682                            Humidity,       any computations.
683                            Pressure,
684                            Voltage
685\\                           ranId           (int) The random-number Id for the histogram
686                                            (same value as where top-level key is ranId)
687\\                           Type            (str) Type of diffraction data, may be 'Debye-Scherrer'
688                                            or 'Bragg-Brentano' .
689hId                         \\               (int) The number assigned to the histogram when
690                                            the project is loaded or edited (can change)
691ranId                       \\               (int) A random number id for the histogram
692                                            that does not change
693Background                  \\               (list) The background is stored as a list with where
694                                            the first item in the list is list and the second
695                                            item is a dict. The list contains the background
696                                            function and its coefficients; the dict contains
697                                            Debye diffuse terms and background peaks.
698                                            (TODO: this needs to be expanded.)
699Data                        \\               (list) The data consist of a list of 6 np.arrays
700                                            containing in order:
701
702                                            0. the x-postions (two-theta in degrees),
703                                            1. the intensity values (Yobs),
704                                            2. the weights for each Yobs value
705                                            3. the computed intensity values (Ycalc)
706                                            4. the background values
707                                            5. Yobs-Ycalc
708======================     ===============  ===========================================================
709
710.. _CWPowder_table:
711
712.. index::
713   single: Powder data CW Instrument Parameters
714
715-----------------------------
716CW Instrument Parameters
717-----------------------------
718
719Instrument Parameters are placed in a list of two dicts,
720where the keys in the first dict are listed below. Note that the dict contents are different for
721constant wavelength (CW) vs. time-of-flight (TOF) histograms.
722The value for each item is a list containing three values: the initial value, the current value
723and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
724cannot be refined. The first and second values are floats unless otherwise noted.
725Items not refined are noted as [*]
726
727.. tabularcolumns:: |l|p{1in}|p{4in}|
728
729========================    ===============  ===========================================================
730  key                       sub-key           explanation
731========================    ===============  ===========================================================
732Instrument Parameters[0]    Type [*]            (str) Histogram type:
733                                                * 'PXC' for constant wavelength x-ray
734                                                * 'PNC' for constant wavelength neutron
735\\                           Bank [*]            (int) Data set number in a multidata file (usually 1)
736\\                           Lam                 (float) Specifies a wavelength in :math:`\\AA`
737\\                           Lam1 [*]            (float) Specifies the primary wavelength in
738                                                :math:`\\AA`, used in place of Lam
739                                                when an :math:`\\alpha_1, \\alpha_2`
740                                                source is used.
741\\                           Lam2 [*]            (float) Specifies the secondary wavelength in
742                                                :math:`\\AA`, used with Lam1
743\\                           I(L2)/I(L1)         (float) Ratio of Lam2 to Lam1, used with Lam1
744\\                           Zero                (float) Two-theta zero correction in *degrees*
745\\                           Azimuth [*]         (float) Azimuthal setting angle for data recorded with differing setting angles
746\\                           U, V, W             (float) Cagliotti profile coefficients
747                                                for Gaussian instrumental broadening, where the
748                                                FWHM goes as
749                                                :math:`U \\tan^2\\theta + V \\tan\\theta + W`
750\\                           X, Y, Z             (float) Cauchy (Lorentzian) instrumental broadening coefficients
751\\                           SH/L                (float) Variant of the Finger-Cox-Jephcoat asymmetric
752                                                peak broadening ratio. Note that this is the
753                                                sum of S/L and H/L where S is
754                                                sample height, H is the slit height and
755                                                L is the goniometer diameter.
756\\                           Polariz.            (float) Polarization coefficient.
757Instrument Parameters[1]                        (empty dict)
758========================    ===============  ===========================================================
759
760.. _TOFPowder_table:
761
762.. index::
763   single: Powder data TOF Instrument Parameters
764
765-----------------------------
766TOF Instrument Parameters
767-----------------------------
768
769Instrument Parameters are also placed in a list of two dicts,
770where the keys in each dict listed below, but here for
771time-of-flight (TOF) histograms.
772The value for each item is a list containing three values: the initial value, the current value
773and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
774cannot be refined. The first and second values are floats unless otherwise noted.
775Items not refined are noted as [*]
776
777.. tabularcolumns:: |l|p{1.5in}|p{4in}|
778
779========================    ===============  ===========================================================
780  key                        sub-key          explanation
781========================    ===============  ===========================================================
782Instrument Parameters[0]    Type [*]            (str) Histogram type:
783                                                * 'PNT' for time of flight neutron
784\\                           Bank                (int) Data set number in a multidata file
785\\                           2-theta [*]         (float) Nominal scattering angle for the detector
786\\                           fltPath [*]         (float) Total flight path source-sample-detector
787\\                           Azimuth [*]         (float) Azimuth angle for detector right hand rotation
788                                                from horizontal away from source
789\\                           difC,difA,          (float) Diffractometer constants for conversion of d-spacing to TOF
790                            difB                in microseconds
791\\                           Zero                (float) Zero point offset (microseconds)
792\\                           alpha               (float) Exponential rise profile coefficients
793\\                           beta-0              (float) Exponential decay profile coefficients
794                            beta-1
795                            beta-q
796\\                           sig-0               (float) Gaussian profile coefficients
797                            sig-1
798                            sig-2
799                            sig-q   
800\\                           X,Y,Z               (float) Lorentzian profile coefficients
801Instrument Parameters[1]    Pdabc               (list of 4 float lists) Originally created for use in gsas as optional tables
802                                                of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation
803                                                from the d-spacing and these tables. The d-true column is apparently unused.
804========================    ===============  ===========================================================
805
806
807.. _PowderRefl_table:
808
809.. index::
810   single: Powder reflection object description
811   single: Data object descriptions; Powder Reflections
812
813Powder Reflection Data Structure
814--------------------------------
815
816For every phase in a histogram, the ``Reflection Lists`` value is a dict
817one element of which is `'RefList'`, which is a np.array containing
818reflections. The columns in that array are documented below.
819
820==========  ====================================================
821  index         explanation
822==========  ====================================================
823 0,1,2          h,k,l (float)
824 3              (int) multiplicity
825 4              (float) d-space, :math:`\\AA`
826 5              (float) pos, two-theta
827 6              (float) sig, Gaussian width
828 7              (float) gam, Lorenzian width
829 8              (float) :math:`F_{obs}^2`
830 9              (float) :math:`F_{calc}^2`
831 10             (float) reflection phase, in degrees
832 11             (float) intensity correction for reflection, this times
833                :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
834 12             (float) Preferred orientation correction
835 13             (float) Transmission (absorption correction)
836 14             (float) Extinction correction
837==========  ====================================================
838
839.. _Xtal_table:
840
841.. index::
842   single: Single Crystal data object description
843   single: Data object descriptions; Single crystal data
844
845Single Crystal Tree Items
846-------------------------
847
848Every single crystal diffraction histogram is stored in the GSAS-II data tree
849with a top-level entry named beginning with the string "HKLF ". The
850diffraction data for that information are directly associated with
851that tree item and there are a series of children to that item. The
852routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
853and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
854load this information into a dictionary where the child tree name is
855used as a key, and the information in the main entry is assigned
856a key of ``Data``, as outlined below.
857
858.. tabularcolumns:: |l|l|p{4in}|
859
860======================  ===============     ====================================================
861  key                      sub-key          explanation
862======================  ===============     ====================================================
863Data                        \\               (dict) that contains the
864                                            reflection table,
865                                            as described in the
866                                            :ref:`Single Crystal Reflections
867                                            <XtalRefl_table>`
868                                            description.
869
870Instrument Parameters       \\               (list) containing two dicts where the possible
871                                            keys in each dict are listed below. The value
872                                            for most items is a list containing two values:
873                                            the initial value, the current value.
874                                            The first and second
875                                            values are floats unless otherwise noted.
876\\                           Lam             (two floats) Specifies a wavelength in :math:`\\AA`
877\\                           Type            (two str values) Histogram type :
878                                            * 'SXC' for constant wavelength x-ray
879                                            * 'SNC' for constant wavelength neutron
880                                            * 'SNT' for time of flight neutron
881\\                           InstrName       (str) A name for the instrument, used in preparing a CIF
882wtFactor                    \\               (float) A weighting factor to increase or decrease
883                                            the leverage of data in the histogram.
884                                            A value of 1.0 weights the data with their
885                                            standard uncertainties and a larger value
886                                            increases the weighting of the data (equivalent
887                                            to decreasing the uncertainties).
888
889hId                         \\               (int) The number assigned to the histogram when
890                                            the project is loaded or edited (can change)
891ranId                       \\               (int) A random number id for the histogram
892                                            that does not change
893======================  ===============     ====================================================
894
895.. _XtalRefl_table:
896
897.. index::
898   single: Single Crystal reflection object description
899   single: Data object descriptions; Single Crystal Reflections
900
901Single Crystal Reflection Data Structure
902----------------------------------------
903
904For every single crystal a histogram, the ``'Data'`` item contains
905the structure factors as an np.array in item `'RefList'`.
906The columns in that array are documented below.
907
908.. tabularcolumns:: |l|p{4in}|
909
910==========  ====================================================
911  index         explanation
912==========  ====================================================
913 0,1,2          (float) h,k,l
914 3              (int) multiplicity
915 4              (float) d-space, :math:`\\AA`
916 5              (float) :math:`F_{obs}^2`
917 6              (float) :math:`\\sigma(F_{obs}^2)`
918 7              (float) :math:`F_{calc}^2`
919 8              (float) :math:`F_{obs}^2T`
920 9              (float) :math:`F_{calc}^2T`
921 10             (float) reflection phase, in degrees
922 11             (float) intensity correction for reflection, this times
923                :math:`F_{obs}^2` or :math:`F_{calc}^2`
924                gives Iobs or Icalc
925==========  ====================================================
926
927.. _Image_table:
928
929.. index::
930   image: Image data object description
931   image: Image object descriptions
932
933Image Data Structure
934--------------------
935
936Every 2-dimensional image is stored in the GSAS-II data tree
937with a top-level entry named beginning with the string "IMG ". The
938image data are directly associated with that tree item and there
939are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
940and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
941load this information into a dictionary where the child tree name is
942used as a key, and the information in the main entry is assigned
943a key of ``Data``, as outlined below.
944
945.. tabularcolumns:: |l|l|p{4in}|
946
947======================  ======================  ====================================================
948  key                      sub-key              explanation
949======================  ======================  ====================================================
950Comments                    \\                   (list of str) Text strings extracted from the original image data
951                                                header or a metafile. These cannot be changed by
952                                                the user; it may be empty.
953Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
954                                                value. Accomodates
955                                                detector orientations other than with the detector
956                                                X-axis
957                                                horizontal.
958\\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
959                                                during image integration multiplied by value. It must have the same size/shape as
960                                                the integrated image. NB: value < 0 for subtraction.
961\\                           calibrant           (str) The material used for determining the position/orientation
962                                                of the image. The data is obtained from :func:`ImageCalibrants`
963                                                and UserCalibrants.py (supplied by user).
964\\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
965\\                           calibskip           (int) The number of expected diffraction lines skipped during the last
966                                                calibration run.
967\\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
968                                                strikes the detector plane as determined by calibration. This point
969                                                does not have to be within the limits of the detector boundaries.
970\\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
971                                                of the image is at the center line otherwise it is at the leading edge.
972\\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
973\\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
974                                                calibration calculations. See pixLimit for details as how point is found.
975\\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
976                                                ring offset at higher angles. Optionally determined by calibration.
977\\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
978\\                           distance            (float) The distance (mm) from sample to detector plane.
979\\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
980                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
981                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
982                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
983                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
984\\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
985\\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
986\\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
987                                                Required for texture calculations.
988\\                           invert_x            (bool) If True display the image with the x-axis inverted.
989\\                           invert_y            (bool) If True display the image with the y-axis inverted.
990\\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
991\\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
992\\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
993                                                intensities obtained during integration.
994\\                           outAzimuths         (int) The number of azimuth pie slices.
995\\                           outChannels         (int) The number of 2-theta steps.
996\\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
997\\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
998                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
999                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
1000                                                Locations are used to construct rings of points for calibration calcualtions.
1001\\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
1002                                                integration using value.
1003\\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
1004                                                diffraction ring with the same d-spacing (dsp)
1005\\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
1006                                                selected by the user,
1007\\                           Range               (list) The minimum & maximum values of the image
1008\\                           rotation            (float) The angle between the x-axis and the vector about which the
1009                                                detector is tilted. Constrained to -180 to 180 deg.
1010\\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
1011                                                calculations.
1012\\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
1013                                                to cause correction to be applied.
1014\\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
1015\\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
1016\\                           showLines           (bool) If True then isplay the integration limits to be used.
1017\\                           size                (list:int) The number of pixels on the image x & y axes
1018\\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
1019\\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
1020\\                           wavelength          (float) The radiation wavelength (:math:`\\AA`) as entered by the user
1021                                                (or someday obtained from the image header).
1022Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
1023                                                to be excluded from integration
1024\\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
1025                                                of which is excluded from recalibration and integration. Only one frame is allowed.
1026\\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
1027                                                from integration.
1028\\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
1029                                                to be excluded from integration.
1030\\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
1031                                                to be excluded from integration.
1032\\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
1033                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
1034\\                           SpotMask            (dict: int & array)
1035                                                'esdMul'(int) number of standard deviations above mean ring intensity to mask
1036                                                'spotMask' (bool array) the spot mask for every pixel in image         
1037
1038Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
1039\\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
1040                                                These will be restricted by space group symmetry; result of strain fit refinement.
1041\\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
1042\\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
1043                                                and are used to determine the strain tensor.
1044                                                The dictionary items are:
1045                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
1046                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
1047                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
1048                                                'Esig': (list: float) Esds for Emat from fitting.
1049                                                'pixLimit': (int) Search range to find highest point on ring for each data point
1050                                                'cutoff': (float) I/Ib cutoff for searching.
1051                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
1052                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
1053                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
1054
1055======================  ======================  ====================================================
1056
1057.. _parmDict_table:
1058
1059.. index::
1060   single: Parameter dictionary
1061
1062Parameter Dictionary
1063-------------------------
1064
1065The parameter dictionary contains all of the variable parameters for the refinement.
1066The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
1067It is prepared in two ways. When loaded from the tree
1068(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
1069:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
1070the values are lists with two elements: ``[value, refine flag]``
1071
1072When loaded from the GPX file (in
1073:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
1074dict is the actual parameter value (usually a float, but sometimes a
1075letter or string flag value (such as I or A for iso/anisotropic).
1076
1077Texture implementation
1078------------------------------
1079
1080There are two different places where texture can be treated in GSAS-II.
1081One is for mitigating the effects of texture in a structural refinement.
1082The other is for texture characterization.
1083
1084For reducing the effect of texture in a structural refinement
1085there are entries labeled preferred orientation in each phase's
1086data tab. Two different
1087approaches can be used for this, the March-Dollase model and
1088spherical harmonics.
1089For the March-Dollase model, one axis in reciprocal space is designated as
1090unique (defaulting to the 001 axis) and reflections are corrected
1091according to the angle they make with this axis depending on
1092the March-Dollase ratio. (If unity, no correction is made).
1093The ratio can be greater than one or less than one depending on if
1094crystallites oriented along the designated axis are
1095overrepresented or underrepresented. For most crystal systems there is an
1096obvious choice for the direction of the unique axis and then only a single
1097term needs to be refined. If the number is close to 1, then the correction
1098is not needed.
1099
1100The second method for reducing the effect of texture in a structural
1101refinement is to create a probability surface as an expansion in
1102terms spherical harmonic functions. Only functions consistent with
1103cylindrical diffraction suymmetry and having texture symmetry
1104consistent with the Laue class of phase are used and are allowed,
1105so the higher the symmetry
1106the fewer terms that are available for a given spherical harmonics order.
1107For use of this correction, select the lowest order that provides
1108refinable terms and perform a refinement. If the texture index remains close to
1109one, then the correction is not needed. If a significant improvement is
1110noted in the profile Rwp, one may wish to see if a higher order expansion
1111gives an even larger improvement.
1112
1113To characterize texture in a material, one needs data collected with the
1114sample at multiple orientations or, for TOF, with detectors at multiple
1115locations around the sample. In this case the detector orientation is given in
1116each histogram's Sample Parameters and the sample's orientation is described
1117with the Euler angles specifed on the phase's Texture tab, which is also
1118where the texture type (cylindrical, rolling,...) and the sherical
1119harmonic order is selected. This should not be used with a single dataset and
1120should not be used if the preferred orientations corrections are used.
1121
1122The coordinate system used for texture characterization is defined where
1123the sample coordinates (Psi, gamma) are defined with an instrument coordinate
1124system (I, J, K) such that I is normal to the diffraction plane and J is coincident with the
1125direction of the incident radiation beam pointing away from the source. We further define
1126a standard set of right-handed goniometer eulerian angles (Omega, Chi, Phi) so that Omega and Phi are
1127rotations about I and Chi is a rotation about J when Omega, Chi, Phi = 0. Finally, as the sample
1128may be mounted so that the sample coordinate system (Is, Js, Ks) does not coincide with
1129the instrument coordinate system (I, J, K), we define three eulerian sample rotation angles
1130(Omega-s, Chi-s, Phi-s) that describe the rotation from (I, J, K) to (Is, Js, Ks). The sample rotation
1131angles are defined so that with the goniometer angles at zero Omega-s and Phi-s are rotations
1132about I and Chi-s is a rotation about J.
1133
1134ISODISTORT implementation
1135------------------------------
1136
1137CIFs prepared with the ISODISTORT web site
1138https://stokes.byu.edu/iso/isodistort_version5.6.1/isodistort.php
1139[B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions." J. Appl. Cryst. 39, 607-614 (2006).]
1140can be read into GSAS-II using import CIF. This will cause constraints to be established for structural distortion modes read from the CIF.
1141At present, of the five types of modes  only displacive(``_iso_displacivemode``...) and occupancy (``_iso_occupancymode``...) are processed. Not yet processed: ``_iso_magneticmode``..., ``_iso_rotationalmode``... & ``_iso_strainmode``...
1142
1143The CIF importer :mod:`G2phase_CIF` implements class :class:`G2phase_CIF.CIFPhaseReader` which offers two methods associated with ISODISTORT (ID) input. Method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_test`
1144checks to see if a CIF block contains the loops with ``_iso_displacivemode_label`` or  ``_iso_occupancymode_label`` items.
1145If so, method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_proc` is called to read and interpret them.
1146The results are placed into the reader object's ``.Phase`` class variable as a dict item with key ``'ISODISTORT'``.
1147
1148Note 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 :func:`G2phase_CIF.ISODISTORT_shortLbl` is used to create a short name for this,
1149such as R5_T1u(a) which is made unique by addition of _n if the short name is duplicated.
1150As each mode is processed, a constraint corresponding to that mode is
1151created and is added to list in the reader object's ``.Constraints`` class variable. Items placed into that list can either be a list, which corresponds to a function (new var) type :ref:`constraint definition <Constraints_table>` entry, or an item can be a dict, which provides help information for each constraint.
1152
1153------------------------------
1154Displacive modes
1155------------------------------
1156
1157The coordinate variables, as named by ISODISTORT, are placed in
1158``.Phase['ISODISTORT']['IsoVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2VarList']``. The mode variables,
1159as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2ModeList']``.
1160[Use ``str(G2VarObj)`` to get the variable name from the G2VarObj object, but note that the phase number, *n*, for the prefix "*n*::" cannot be determined as the phase number is not yet assigned.]
1161
1162Displacive modes are a bit complex in that they relate to delta displacements, relative to an offset value for each coordinate, and because the modes are normalized, while GSAS-II also uses displacements, but these are added to the coordinates after each refinement cycle and the delta values are set to zero. ISODISTORT uses fixed offsets (subtracted from the actual position to obtain the delta values) that are taken from ``_iso_coordinate_formula`` and these are placed in ``.Phase['ISODISTORT']['ParentStructure]`` (keyed by atom label). The normalization factors (which the delta values are divided by) are taken from ``_iso_displacivemodenorm_value`` and are placed in ``.Phase['ISODISTORT']['NormList']`` in the same order as as ``...['IsoModeList']`` and
1163``...['G2ModeList']``.
1164
1165The CIF contains a sparse matrix, from the ``loop_`` containing
1166``_iso_displacivemodematrix_value`` which provides the equations for determining the mode values from the coordinates, that matrix is placed in ``.Phase['ISODISTORT']['Mode2VarMatrix']``. The matrix is inverted to produce
1167``.Phase['ISODISTORT']['Var2ModeMatrix']``, which determines how to compute the
1168mode values from the delta coordinate values. These values are used for the
1169in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1170values, the latter with s.u. values.
1171
1172
1173------------------------------
1174Occupancy modes
1175------------------------------
1176
1177
1178The delta occupancy variables, as named by ISODISTORT, are placed in
1179``.Phase['ISODISTORT']['OccVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2OccVarList']``. The mode variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['OccModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2OccModeList']``.
1180
1181Occupancy modes, like Displacive modes, are also refined as delta values.  However, GSAS-II directly refines the fractional occupancies.
1182Offset values for each atom, are taken from ``_iso_occupancy_formula`` and are placed in
1183``.Phase['ISODISTORT']['ParentOcc]``.
1184(Offset values are subtracted from the actual position to obtain the delta values.)
1185Modes are normalized (where the mode values are divided by the normalization factor)
1186are taken from ``_iso_occupancymodenorm_value`` and are placed in ``.Phase['ISODISTORT']['OccNormList']`` in the same order as as ``...['OccModeList']`` and
1187``...['G2OccModeList']``.
1188
1189The CIF contains a sparse matrix, from the ``loop_`` containing
1190``_iso_occupancymodematrix_value``, which provides the equations for determining the mode values from the coordinates. That matrix is placed in ``.Phase['ISODISTORT']['Occ2VarMatrix']``. The matrix is inverted to produce
1191``.Phase['ISODISTORT']['Var2OccMatrix']``, which determines how to compute the
1192mode values from the delta coordinate values.
1193
1194
1195------------------------------
1196Mode Computations
1197------------------------------
1198
1199Constraints are processed after the CIF has been read in
1200:meth:`GSASIIdataGUI.GSASII.OnImportPhase` or 
1201:meth:`GSASIIscriptable.G2Project.add_phase` by moving them from the reader
1202object's ``.Constraints`` class variable to
1203the Constraints tree entry's ['Phase'] list (for list items defining constraints) or
1204the Constraints tree entry's ['_Explain'] dict (for dict items defining constraint help information)
1205
1206The information in ``.Phase['ISODISTORT']`` is used
1207in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1208values, the latter with s.u. values. This can be called from the Constraints and Phase/Atoms tree items.
1209
1210Before each refinement, constraints are processed as
1211:ref:`described elsewhere <Constraints_processing>`. After a refinement
1212is complete, :func:`GSASIImapvars.PrintIndependentVars` shows the
1213shifts and s.u.'s on the refined modes, using GSAS-II values, but
1214:func:`GSASIIstrIO.PrintISOmodes` prints the ISODISTORT modes as computed
1215in the web site.
1216
1217
1218.. _ParameterLimits:
1219
1220.. index::
1221   single: Parameter limits
1222
1223Parameter Limits
1224------------------------------
1225
1226One of the most often requested "enhancements" for GSAS-II would be the inclusion
1227of constraints to force parameters such as occupancies or Uiso values to stay within
1228expected ranges. While it is possible for users to supply their own restraints that would
1229perform this by supplying an appropriate expression with the "General" restraints, the
1230GSAS-II authors do not feel that use of restraints or constraints are a good solution for
1231this common problem where parameters refine to non-physical values. This is because when
1232this occurs, most likely one of the following cases is occurring:
1233
1234#. there is a significant problem
1235   with the model, for example for an x-ray fit if an O atom is placed where a S is actually
1236   present, the Uiso will refine artificially small or the occupancy much larger than unity
1237   to try to compensate for the missing electrons; or
1238 
1239#. the data are simply insensitive
1240   to the parameter or combination of parameters, for example unless very high-Q data
1241   are included, the effects of a occupancy and Uiso value can have compensating effects,
1242   so an assumption must be made; likewise, with neutron data natural-abundance V atoms
1243   are nearly invisible due to weak coherent scattering. No parameters can be fit for a
1244   V atom with neutrons.
1245
1246#. the parameter is non-physical (such as a negative Uiso value) but within
1247   two sigma (sigma = standard uncertainty, aka e.s.d.) of a reasonable value,
1248   in which case the
1249   value is not problematic as it is experimentally indistinguishable from an
1250   expected value. 
1251
1252#. there is a systematic problem with the data (experimental error)
1253
1254In all these cases, this situation needs to be reviewed by a crystallographer to decide
1255how to best determine a structural model for these data. An implementation with a constraint
1256or restraint is likely to simply hide the problem from the user, making it more probable
1257that a poor model choice is obtained.
1258
1259What GSAS-II does implement is to allow users to specify ranges for parameters
1260that works by disabling
1261refinement of parameters that refine beyond either a lower limit or an upper limit, where
1262either or both may be optionally specified. Parameters limits are specified in the Controls
1263tree entry in dicts named as ``Controls['parmMaxDict']`` and ``Controls['parmMinDict']``, where
1264the keys are :class:`G2VarObj` objects corresponding to standard GSAS-II variable
1265(see :func:`getVarDescr` and :func:`CompileVarDesc`) names, where a
1266wildcard ('*') may optionally be used for histogram number or atom number
1267(phase number is intentionally not  allowed as a wildcard as it makes little sense
1268to group the same parameter together different phases). Note
1269that :func:`prmLookup` is used to see if a name matches a wildcard. The upper or lower limit
1270is placed into these dicts as a float value. These values can be edited using the window
1271created by the Calculate/"View LS parms" menu command or in scripting with the
1272:meth:`GSASIIscriptable.G2Project.set_Controls` function.
1273In the GUI, a checkbox labeled "match all histograms/atoms" is used to insert a wildcard
1274into the appropriate part of the variable name.
1275
1276When a refinement is conducted, routine :func:`GSASIIstrMain.dropOOBvars` is used to
1277find parameters that have refined to values outside their limits. If this occurs, the parameter
1278is set to the limiting value and the variable name is added to a list of frozen variables
1279(as a :class:`G2VarObj` objects) kept in a list in the
1280``Controls['parmFrozen']`` dict. In a sequential refinement, this is kept separate for
1281each histogram as a list in
1282``Controls['parmFrozen'][histogram]`` (where the key is the histogram name) or as a list in
1283``Controls['parmFrozen']['FrozenList']`` for a non-sequential fit.
1284This allows different variables
1285to be frozen in each section of a sequential fit.
1286Frozen parameters are not included in refinements through removal from the
1287list of parameters to be refined (``varyList``) in :func:`GSASIIstrMain.Refine` or
1288:func:`GSASIIstrMain.SeqRefine`.
1289The data window for the Controls tree item shows the number of Frozen variables and
1290the individual variables can be viewed with the Calculate/"View LS parms" menu window or
1291obtained with :meth:`GSASIIscriptable.G2Project.get_Frozen`.
1292Once a variable is frozen, it will not be refined in any
1293future refinements unless the the variable is removed (manually) from the list. This can also
1294be done with the Calculate/"View LS parms" menu window or
1295:meth:`GSASIIscriptable.G2Project.set_Frozen`.
1296
1297
1298.. seealso::
1299  :class:`G2VarObj`
1300  :func:`getVarDescr`
1301  :func:`CompileVarDesc`
1302  :func:`prmLookup`
1303  :class:`GSASIIctrlGUI.ShowLSParms`
1304  :class:`GSASIIctrlGUI.VirtualVarBox`
1305  :func:`GSASIIstrIO.SetUsedHistogramsAndPhases`
1306  :func:`GSASIIstrIO.SaveUpdatedHistogramsAndPhases`
1307  :func:`GSASIIstrIO.SetSeqResult`
1308  :func:`GSASIIstrMain.dropOOBvars`
1309  :meth:`GSASIIscriptable.G2Project.set_Controls`
1310  :meth:`GSASIIscriptable.G2Project.get_Frozen`
1311  :meth:`GSASIIscriptable.G2Project.set_Frozen`
1312
1313*Classes and routines*
1314----------------------
1315
1316'''
1317from __future__ import division, print_function
1318import platform
1319import re
1320import random as ran
1321import sys
1322import os.path as ospath
1323if '2' in platform.python_version_tuple()[0]:
1324    import cPickle
1325else:
1326    import pickle as cPickle
1327import GSASIIpath
1328import GSASIImath as G2mth
1329import GSASIIspc as G2spc
1330import numpy as np
1331
1332GSASIIpath.SetVersionNumber("$Revision$")
1333
1334DefaultControls = {
1335    'deriv type':'analytic Hessian',
1336    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
1337    'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
1338    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
1339    'Author':'no name',
1340    'FreePrm1':'Sample humidity (%)',
1341    'FreePrm2':'Sample voltage (V)',
1342    'FreePrm3':'Applied load (MN)',
1343    'ShowCell':False,
1344    }
1345'''Values to be used as defaults for the initial contents of the ``Controls``
1346data tree item.
1347'''
1348def StripUnicode(string,subs='.'):
1349    '''Strip non-ASCII characters from strings
1350
1351    :param str string: string to strip Unicode characters from
1352    :param str subs: character(s) to place into string in place of each
1353      Unicode character. Defaults to '.'
1354
1355    :returns: a new string with only ASCII characters
1356    '''
1357    s = ''
1358    for c in string:
1359        if ord(c) < 128:
1360            s += c
1361        else:
1362            s += subs
1363    return s
1364#    return s.encode('ascii','replace')
1365
1366def MakeUniqueLabel(lbl,labellist):
1367    '''Make sure that every a label is unique against a list by adding
1368    digits at the end until it is not found in list.
1369
1370    :param str lbl: the input label
1371    :param list labellist: the labels that have already been encountered
1372    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
1373      ``_10-99``, etc.) appended at the end
1374    '''
1375    lbl = StripUnicode(lbl.strip(),'_')
1376    if not lbl: # deal with a blank label
1377        lbl = '_1'
1378    if lbl not in labellist:
1379        labellist.append(lbl)
1380        return lbl
1381    i = 1
1382    prefix = lbl
1383    if '_' in lbl:
1384        prefix = lbl[:lbl.rfind('_')]
1385        suffix = lbl[lbl.rfind('_')+1:]
1386        try:
1387            i = int(suffix)+1
1388        except: # suffix could not be parsed
1389            i = 1
1390            prefix = lbl
1391    while prefix+'_'+str(i) in labellist:
1392        i += 1
1393    else:
1394        lbl = prefix+'_'+str(i)
1395        labellist.append(lbl)
1396    return lbl
1397
1398PhaseIdLookup = {}
1399'''dict listing phase name and random Id keyed by sequential phase index as a str;
1400best to access this using :func:`LookupPhaseName`
1401'''
1402PhaseRanIdLookup = {}
1403'''dict listing phase sequential index keyed by phase random Id;
1404best to access this using :func:`LookupPhaseId`
1405'''
1406HistIdLookup = {}
1407'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
1408best to access this using :func:`LookupHistName`
1409'''
1410HistRanIdLookup = {}
1411'''dict listing histogram sequential index keyed by histogram random Id;
1412best to access this using :func:`LookupHistId`
1413'''
1414AtomIdLookup = {}
1415'''dict listing for each phase index as a str, the atom label and atom random Id,
1416keyed by atom sequential index as a str;
1417best to access this using :func:`LookupAtomLabel`
1418'''
1419AtomRanIdLookup = {}
1420'''dict listing for each phase the atom sequential index keyed by atom random Id;
1421best to access this using :func:`LookupAtomId`
1422'''
1423ShortPhaseNames = {}
1424'''a dict containing a possibly shortened and when non-unique numbered
1425version of the phase name. Keyed by the phase sequential index.
1426'''
1427ShortHistNames = {}
1428'''a dict containing a possibly shortened and when non-unique numbered
1429version of the histogram name. Keyed by the histogram sequential index.
1430'''
1431
1432#VarDesc = {}  # removed 1/30/19 BHT as no longer needed (I think)
1433#''' This dictionary lists descriptions for GSAS-II variables,
1434#as set in :func:`CompileVarDesc`. See that function for a description
1435#for how keys and values are written.
1436#'''
1437
1438reVarDesc = {}
1439''' This dictionary lists descriptions for GSAS-II variables where
1440keys are compiled regular expressions that will match the name portion
1441of a parameter name. Initialized in :func:`CompileVarDesc`.
1442'''
1443
1444reVarStep = {}
1445''' This dictionary lists the preferred step size for numerical
1446derivative computation w/r to a GSAS-II variable. Keys are compiled
1447regular expressions and values are the step size for that parameter.
1448Initialized in :func:`CompileVarDesc`.
1449'''
1450# create a default space group object for P1; N.B. fails when building documentation
1451try:
1452    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1453except:
1454    pass
1455
1456def GetPhaseNames(fl):
1457    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1458    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1459
1460    :param file fl: opened .gpx file
1461    :return: list of phase names
1462    '''
1463    PhaseNames = []
1464    while True:
1465        try:
1466            data = cPickle.load(fl)
1467        except EOFError:
1468            break
1469        datum = data[0]
1470        if 'Phases' == datum[0]:
1471            for datus in data[1:]:
1472                PhaseNames.append(datus[0])
1473    fl.seek(0)          #reposition file
1474    return PhaseNames
1475
1476def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1477    '''Create a new phase dict with default values for various parameters
1478
1479    :param str Name: Name for new Phase
1480
1481    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1482      defaults to data for P 1
1483
1484    :param list cell: unit cell parameter list; defaults to
1485      [1.0,1.0,1.0,90.,90,90.,1.]
1486
1487    '''
1488    if SGData is None: SGData = P1SGData
1489    if cell is None: cell=[1.0,1.0,1.0,90.,90.,90.,1.]
1490    phaseData = {
1491        'ranId':ran.randint(0,sys.maxsize),
1492        'General':{
1493            'Name':Name,
1494            'Type':'nuclear',
1495            'Modulated':False,
1496            'AtomPtrs':[3,1,7,9],
1497            'SGData':SGData,
1498            'Cell':[False,]+cell,
1499            'Pawley dmin':1.0,
1500            'Data plot type':'None',
1501            'SH Texture':{
1502                'Order':0,
1503                'Model':'cylindrical',
1504                'Sample omega':[False,0.0],
1505                'Sample chi':[False,0.0],
1506                'Sample phi':[False,0.0],
1507                'SH Coeff':[False,{}],
1508                'SHShow':False,
1509                'PFhkl':[0,0,1],
1510                'PFxyz':[0,0,1],
1511                'PlotType':'Pole figure',
1512                'Penalty':[['',],0.1,False,1.0]}},
1513        'Atoms':[],
1514        'Drawing':{},
1515        'Histograms':{},
1516        'Pawley ref':[],
1517        'RBModels':{},
1518        }
1519    if Super and Super.get('Use',False):
1520        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1521        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])[1]
1522        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1523
1524    return phaseData
1525
1526def ReadCIF(URLorFile):
1527    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1528    (from James Hester).
1529    The open routine gets confused with DOS names that begin with a letter and colon
1530    "C:\\dir\" so this routine will try to open the passed name as a file and if that
1531    fails, try it as a URL
1532
1533    :param str URLorFile: string containing a URL or a file name. Code will try first
1534      to open it as a file and then as a URL.
1535
1536    :returns: a PyCifRW CIF object.
1537    '''
1538    import CifFile as cif # PyCifRW from James Hester
1539
1540    # alternate approach:
1541    #import urllib
1542    #ciffile = 'file:'+urllib.pathname2url(filename)
1543
1544    try:
1545        fp = open(URLorFile,'r')
1546        cf = cif.ReadCif(fp)
1547        fp.close()
1548        return cf
1549    except IOError:
1550        return cif.ReadCif(URLorFile)
1551
1552def TestIndexAll():
1553    '''Test if :func:`IndexAllIds` has been called to index all phases and
1554    histograms (this is needed before :func:`G2VarObj` can be used.
1555
1556    :returns: Returns True if indexing is needed.
1557    '''
1558    if PhaseIdLookup or AtomIdLookup or HistIdLookup:
1559        return False
1560    return True
1561       
1562def IndexAllIds(Histograms,Phases):
1563    '''Scan through the used phases & histograms and create an index
1564    to the random numbers of phases, histograms and atoms. While doing this,
1565    confirm that assigned random numbers are unique -- just in case lightning
1566    strikes twice in the same place.
1567
1568    Note: this code assumes that the atom random Id (ranId) is the last
1569    element each atom record.
1570
1571    This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
1572    (which loads the histograms and phases from a GPX file),
1573    :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
1574    (which loads the histograms and phases from the data tree.) and
1575    :meth:`GSASIIconstrGUI.UpdateConstraints`
1576    (which displays & edits the constraints in a GUI)
1577
1578    TODO: do we need a lookup for rigid body variables?
1579    '''
1580    # process phases and atoms
1581    PhaseIdLookup.clear()
1582    PhaseRanIdLookup.clear()
1583    AtomIdLookup.clear()
1584    AtomRanIdLookup.clear()
1585    ShortPhaseNames.clear()
1586    for ph in Phases:
1587        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1588        ranId = Phases[ph]['ranId']
1589        while ranId in PhaseRanIdLookup:
1590            # Found duplicate random Id! note and reassign
1591            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1592            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1593        pId = str(Phases[ph]['pId'])
1594        PhaseIdLookup[pId] = (ph,ranId)
1595        PhaseRanIdLookup[ranId] = pId
1596        shortname = ph  #[:10]
1597        while shortname in ShortPhaseNames.values():
1598            shortname = ph[:8] + ' ('+ pId + ')'
1599        ShortPhaseNames[pId] = shortname
1600        AtomIdLookup[pId] = {}
1601        AtomRanIdLookup[pId] = {}
1602        for iatm,at in enumerate(Phases[ph]['Atoms']):
1603            ranId = at[cia+8]
1604            while ranId in AtomRanIdLookup[pId]: # check for dups
1605                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1606                at[cia+8] = ranId = ran.randint(0,sys.maxsize)
1607            AtomRanIdLookup[pId][ranId] = str(iatm)
1608            if Phases[ph]['General']['Type'] == 'macromolecular':
1609                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1610            else:
1611                label = at[ct-1]
1612            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1613    # process histograms
1614    HistIdLookup.clear()
1615    HistRanIdLookup.clear()
1616    ShortHistNames.clear()
1617    for hist in Histograms:
1618        ranId = Histograms[hist]['ranId']
1619        while ranId in HistRanIdLookup:
1620            # Found duplicate random Id! note and reassign
1621            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1622            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1623        hId = str(Histograms[hist]['hId'])
1624        HistIdLookup[hId] = (hist,ranId)
1625        HistRanIdLookup[ranId] = hId
1626        shortname = hist[:15]
1627        while shortname in ShortHistNames.values():
1628            shortname = hist[:11] + ' ('+ hId + ')'
1629        ShortHistNames[hId] = shortname
1630
1631def LookupAtomId(pId,ranId):
1632    '''Get the atom number from a phase and atom random Id
1633
1634    :param int/str pId: the sequential number of the phase
1635    :param int ranId: the random Id assigned to an atom
1636
1637    :returns: the index number of the atom (str)
1638    '''
1639    if not AtomRanIdLookup:
1640        raise Exception('Error: LookupAtomId called before IndexAllIds was run')
1641    if pId is None or pId == '':
1642        raise KeyError('Error: phase is invalid (None or blank)')
1643    pId = str(pId)
1644    if pId not in AtomRanIdLookup:
1645        raise KeyError('Error: LookupAtomId does not have phase '+pId)
1646    if ranId not in AtomRanIdLookup[pId]:
1647        raise KeyError('Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']')
1648    return AtomRanIdLookup[pId][ranId]
1649
1650def LookupAtomLabel(pId,index):
1651    '''Get the atom label from a phase and atom index number
1652
1653    :param int/str pId: the sequential number of the phase
1654    :param int index: the index of the atom in the list of atoms
1655
1656    :returns: the label for the atom (str) and the random Id of the atom (int)
1657    '''
1658    if not AtomIdLookup:
1659        raise Exception('Error: LookupAtomLabel called before IndexAllIds was run')
1660    if pId is None or pId == '':
1661        raise KeyError('Error: phase is invalid (None or blank)')
1662    pId = str(pId)
1663    if pId not in AtomIdLookup:
1664        raise KeyError('Error: LookupAtomLabel does not have phase '+pId)
1665    if index not in AtomIdLookup[pId]:
1666        raise KeyError('Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']')
1667    return AtomIdLookup[pId][index]
1668
1669def LookupPhaseId(ranId):
1670    '''Get the phase number and name from a phase random Id
1671
1672    :param int ranId: the random Id assigned to a phase
1673    :returns: the sequential Id (pId) number for the phase (str)
1674    '''
1675    if not PhaseRanIdLookup:
1676        raise Exception('Error: LookupPhaseId called before IndexAllIds was run')
1677    if ranId not in PhaseRanIdLookup:
1678        raise KeyError('Error: LookupPhaseId does not have ranId '+str(ranId))
1679    return PhaseRanIdLookup[ranId]
1680
1681def LookupPhaseName(pId):
1682    '''Get the phase number and name from a phase Id
1683
1684    :param int/str pId: the sequential assigned to a phase
1685    :returns:  (phase,ranId) where phase is the name of the phase (str)
1686      and ranId is the random # id for the phase (int)
1687    '''
1688    if not PhaseIdLookup:
1689        raise Exception('Error: LookupPhaseName called before IndexAllIds was run')
1690    if pId is None or pId == '':
1691        raise KeyError('Error: phase is invalid (None or blank)')
1692    pId = str(pId)
1693    if pId not in PhaseIdLookup:
1694        raise KeyError('Error: LookupPhaseName does not have index '+pId)
1695    return PhaseIdLookup[pId]
1696
1697def LookupHistId(ranId):
1698    '''Get the histogram number and name from a histogram random Id
1699
1700    :param int ranId: the random Id assigned to a histogram
1701    :returns: the sequential Id (hId) number for the histogram (str)
1702    '''
1703    if not HistRanIdLookup:
1704        raise Exception('Error: LookupHistId called before IndexAllIds was run')
1705    if ranId not in HistRanIdLookup:
1706        raise KeyError('Error: LookupHistId does not have ranId '+str(ranId))
1707    return HistRanIdLookup[ranId]
1708
1709def LookupHistName(hId):
1710    '''Get the histogram number and name from a histogram Id
1711
1712    :param int/str hId: the sequential assigned to a histogram
1713    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1714      and ranId is the random # id for the histogram (int)
1715    '''
1716    if not HistIdLookup:
1717        raise Exception('Error: LookupHistName called before IndexAllIds was run')
1718    if hId is None or hId == '':
1719        raise KeyError('Error: histogram is invalid (None or blank)')
1720    hId = str(hId)
1721    if hId not in HistIdLookup:
1722        raise KeyError('Error: LookupHistName does not have index '+hId)
1723    return HistIdLookup[hId]
1724
1725def fmtVarDescr(varname):
1726    '''Return a string with a more complete description for a GSAS-II variable
1727
1728    :param str varname: A full G2 variable name with 2 or 3 or 4
1729       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1730
1731    :returns: a string with the description
1732    '''
1733    s,l = VarDescr(varname)
1734    return s+": "+l
1735
1736def VarDescr(varname):
1737    '''Return two strings with a more complete description for a GSAS-II variable
1738
1739    :param str name: A full G2 variable name with 2 or 3 or 4
1740       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1741
1742    :returns: (loc,meaning) where loc describes what item the variable is mapped
1743      (phase, histogram, etc.) and meaning describes what the variable does.
1744    '''
1745
1746    # special handling for parameter names without a colon
1747    # for now, assume self-defining
1748    if varname.find(':') == -1:
1749        return "Global",varname
1750
1751    l = getVarDescr(varname)
1752    if not l:
1753        return ("invalid variable name ("+str(varname)+")!"),""
1754#        return "invalid variable name!",""
1755
1756    if not l[-1]:
1757        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1758
1759    if len(l) == 3:         #SASD variable name!
1760        s = 'component:'+l[1]
1761        return s,l[-1]
1762    s = ""
1763    if l[0] is not None and l[1] is not None: # HAP: keep short
1764        if l[2] == "Scale": # fix up ambigous name
1765            l[5] = "Phase fraction"
1766        if l[0] == '*':
1767            lbl = 'Seq. ref.'
1768        else:
1769            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1770        if l[1] == '*':
1771            hlbl = 'Seq. ref.'
1772        else:
1773            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1774        if hlbl[:4] == 'HKLF':
1775            hlbl = 'Xtl='+hlbl[5:]
1776        elif hlbl[:4] == 'PWDR':
1777            hlbl = 'Pwd='+hlbl[5:]
1778        else:
1779            hlbl = 'Hist='+hlbl
1780        s = "Ph="+str(lbl)+" * "+str(hlbl)
1781    else:
1782        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1783            l[5] = "Scale factor"
1784        if l[2] == 'Back': # background parameters are "special", alas
1785            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1786            l[-1] += ' #'+str(l[3])
1787        elif l[4] is not None: # rigid body parameter or modulation parm
1788            lbl = ShortPhaseNames.get(l[0],'phase?')
1789            if 'RB' in l[2]:    #rigid body parm
1790                s = "RB body #"+str(l[3])+" (type "+str(l[4])+") in "+str(lbl) + ','
1791            else: #modulation parm
1792                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1793        elif l[3] is not None: # atom parameter,
1794            lbl = ShortPhaseNames.get(l[0],'phase?')
1795            try:
1796                albl = LookupAtomLabel(l[0],l[3])[0]
1797            except KeyError:
1798                albl = 'Atom?'
1799            s = "Atom "+str(albl)+" in "+str(lbl)
1800        elif l[0] == '*':
1801            s = "All phases "
1802        elif l[0] is not None:
1803            lbl = ShortPhaseNames.get(l[0],'phase?')
1804            s = "Phase "+str(lbl)
1805        elif l[1] == '*':
1806            s = 'All hists'
1807        elif l[1] is not None:
1808            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1809            if hlbl[:4] == 'HKLF':
1810                hlbl = 'Xtl='+hlbl[5:]
1811            elif hlbl[:4] == 'PWDR':
1812                hlbl = 'Pwd='+hlbl[5:]
1813            else:
1814                hlbl = 'Hist='+hlbl
1815            s = str(hlbl)
1816    if not s:
1817        s = 'Global'
1818    return s,l[-1]
1819
1820def getVarDescr(varname):
1821    '''Return a short description for a GSAS-II variable
1822
1823    :param str name: A full G2 variable name with 2 or 3 or 4
1824       colons (<p>:<h>:name[:<a1>][:<a2>])
1825
1826    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1827      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1828      the histogram number and the atom number; `name` will always be
1829      a str; and `description` is str or `None`.
1830      If the variable name is incorrectly formed (for example, wrong
1831      number of colons), `None` is returned instead of a list.
1832    '''
1833    l = varname.split(':')
1834    if len(l) == 2:     #SASD parameter name
1835        return varname,l[0],getDescr(l[1])
1836    if len(l) == 3:
1837        l += [None,None]
1838    elif len(l) == 4:
1839        l += [None]
1840    elif len(l) != 5:
1841        return None
1842    for i in (0,1,3,4):
1843        if l[i] == "":
1844            l[i] = None
1845    l += [getDescr(l[2])]
1846    return l
1847
1848def CompileVarDesc():
1849    '''Set the values in the variable lookup tables
1850    (:attr:`reVarDesc` and :attr:`reVarStep`).
1851    This is called in :func:`getDescr` and :func:`getVarStep` so this
1852    initialization is always done before use.
1853
1854    Note that keys may contain regular expressions, where '[xyz]'
1855    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range
1856    of values). '.*' matches any string. For example::
1857
1858    'AUiso':'Atomic isotropic displacement parameter',
1859
1860    will match variable ``'p::AUiso:a'``.
1861    If parentheses are used in the key, the contents of those parentheses can be
1862    used in the value, such as::
1863
1864    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1865
1866    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1867    in the value when used.
1868
1869    '''
1870    if reVarDesc: return # already done
1871    for key,value in {
1872        # derived or other sequential vars
1873        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1874        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1875        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1876        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1877        # ambiguous, alas:
1878        'Scale' : 'Phase or Histogram scale factor',
1879        # Phase vars (p::<var>)
1880        'A([0-5])' : ('Reciprocal metric tensor component \\1',1e-5),
1881        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1882        # Atom vars (p::<var>:a)
1883        'dA([xyz])$' : ('change to atomic coordinate, \\1',1e-6),
1884        'A([xyz])$' : '\\1 fractional atomic coordinate',
1885        'AUiso':('Atomic isotropic displacement parameter',1e-4),
1886        'AU([123][123])':('Atomic anisotropic displacement parameter U\\1',1e-4),
1887        'Afrac': ('Atomic site fraction parameter',1e-5),
1888        'Amul': 'Atomic site multiplicity value',
1889        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1890        # Hist (:h:<var>) & Phase (HAP) vars (p:h:<var>)
1891        'Back': 'Background term',
1892        'BkPkint;(.*)':'Background peak #\\1 intensity',
1893        'BkPkpos;(.*)':'Background peak #\\1 position',
1894        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1895        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1896#        'Back File' : 'Background file name',
1897        'BF mult' : 'Background file multiplier',
1898        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1899        'D([123][123])' : 'Anisotropic strain coef. \\1',
1900        'Extinction' : 'Extinction coef.',
1901        'MD' : 'March-Dollase coef.',
1902        'Mustrain;.*' : 'Microstrain coef.',
1903        'Size;.*' : 'Crystallite size value',
1904        'eA$' : 'Cubic mustrain value',
1905        'Ep$' : 'Primary extinction',
1906        'Es$' : 'Secondary type II extinction',
1907        'Eg$' : 'Secondary type I extinction',
1908        'Flack' : 'Flack parameter',
1909        'TwinFr' : 'Twin fraction',
1910        'Layer Disp'  : 'Layer displacement along beam',
1911        #Histogram vars (:h:<var>)
1912        'Absorption' : 'Absorption coef.',
1913        'Displace([XY])' : ('Debye-Scherrer sample displacement \\1',0.1),
1914        'Lam' : ('Wavelength',1e-6),
1915        'I\\(L2\\)\\/I\\(L1\\)' : ('Ka2/Ka1 intensity ratio',0.001),
1916        'Polariz\\.' : ('Polarization correction',1e-3),
1917        'SH/L' : ('FCJ peak asymmetry correction',1e-4),
1918        '([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),
1919        '([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),
1920        'Zero' : 'Debye-Scherrer zero correction',
1921        'Shift' : 'Bragg-Brentano sample displ.',
1922        'SurfRoughA' : 'Bragg-Brenano surface roughness A',
1923        'SurfRoughB' : 'Bragg-Brenano surface roughness B',
1924        'Transparency' : 'Bragg-Brentano sample tranparency',
1925        'DebyeA' : 'Debye model amplitude',
1926        'DebyeR' : 'Debye model radius',
1927        'DebyeU' : 'Debye model Uiso',
1928        'RBV.*' : 'Vector rigid body parameter',
1929        'RBRO([aijk])' : 'Residue rigid body orientation parameter \\1',
1930        'RBRP([xyz])' : 'Residue rigid body \\1 position parameter',
1931        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1932        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1933        'RBRU' : 'Residue rigid body group Uiso param.',
1934        'constr([0-9]*)' : 'Parameter from constraint',
1935        'nv-([^_]+)_*' : 'New variable constraint parameter named \\1',
1936        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1937        'mV([0-2])$' : 'Modulation vector component \\1',
1938        'Fsin'  :   'Sin site fraction modulation',
1939        'Fcos'  :   'Cos site fraction modulation',
1940        'Fzero'  :   'Crenel function offset',      #may go away
1941        'Fwid'   :   'Crenel function width',
1942        'Tmin'   :   'ZigZag/Block min location',
1943        'Tmax'   :   'ZigZag/Block max location',
1944        '([XYZ])max': 'ZigZag/Block max value for \\1',
1945        '([XYZ])sin'  : 'Sin position wave for \\1',
1946        '([XYZ])cos'  : 'Cos position wave for \\1',
1947        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1948        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1949        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1950        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1951        # PDF peak parms (l:<var>;l = peak no.)
1952        'PDFpos'  : 'PDF peak position',
1953        'PDFmag'  : 'PDF peak magnitude',
1954        'PDFsig'  : 'PDF peak std. dev.',
1955        # SASD vars (l:<var>;l = component)
1956        'Aspect ratio' : 'Particle aspect ratio',
1957        'Length' : 'Cylinder length',
1958        'Diameter' : 'Cylinder/disk diameter',
1959        'Thickness' : 'Disk thickness',
1960        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1961        'Dist' : 'Interparticle distance',
1962        'VolFr' : 'Dense scatterer volume fraction',
1963        'epis' : 'Sticky sphere epsilon',
1964        'Sticky' : 'Stickyness',
1965        'Depth' : 'Well depth',
1966        'Width' : 'Well width',
1967        'Volume' : 'Particle volume',
1968        'Radius' : 'Sphere/cylinder/disk radius',
1969        'Mean' : 'Particle mean radius',
1970        'StdDev' : 'Standard deviation in Mean',
1971        'G$': 'Guinier prefactor',
1972        'Rg$': 'Guinier radius of gyration',
1973        'B$': 'Porod prefactor',
1974        'P$': 'Porod power',
1975        'Cutoff': 'Porod cutoff',
1976        'PkInt': 'Bragg peak intensity',
1977        'PkPos': 'Bragg peak position',
1978        'PkSig': 'Bragg peak sigma',
1979        'PkGam': 'Bragg peak gamma',
1980        'e([12][12])' : 'strain tensor e\\1',   # strain vars e11, e22, e12
1981        'Dcalc': 'Calc. d-spacing',
1982        'Back$': 'background parameter',
1983        'pos$': 'peak position',
1984        'int$': 'peak intensity',
1985        'WgtFrac':'phase weight fraction',
1986        'alpha':'TOF profile term',
1987        'alpha-[01]':'Pink profile term',
1988        'beta-[01q]':'TOF/Pink profile term',
1989        'sig-[012q]':'TOF profile term',
1990        'dif[ABC]':'TOF to d-space calibration',
1991        'C\\([0-9]*,[0-9]*\\)' : 'spherical harmonics preferred orientation coef.',
1992        'Pressure': 'Pressure level for measurement in MPa',
1993        'Temperature': 'T value for measurement, K',
1994        'FreePrm([123])': 'User defined measurement parameter \\1',
1995        'Gonio. radius': 'Distance from sample to detector, mm',
1996        }.items():
1997        # Needs documentation: HAP: LayerDisp, LeBail, newLeBail
1998        # hist: Azimuth, Chi, Omega, Phi, Bank, nDebye, nPeaks
1999       
2000        if len(value) == 2:
2001            #VarDesc[key] = value[0]
2002            reVarDesc[re.compile(key)] = value[0]
2003            reVarStep[re.compile(key)] = value[1]
2004        else:
2005            #VarDesc[key] = value
2006            reVarDesc[re.compile(key)] = value
2007
2008def removeNonRefined(parmList):
2009    '''Remove items from variable list that are not refined and should not
2010    appear as options for constraints
2011
2012    :param list parmList: a list of strings of form "p:h:VAR:a" where
2013      VAR is the variable name
2014
2015    :returns: a list after removing variables where VAR matches a
2016      entry in local variable NonRefinedList
2017    '''
2018    NonRefinedList = ['Omega','Type','Chi','Phi', 'Azimuth','Gonio. radius',
2019                          'Lam1','Lam2','Back','Temperature','Pressure',
2020                          'FreePrm1','FreePrm2','FreePrm3',
2021                          'Source','nPeaks','LeBail','newLeBail','Bank',
2022                          'nDebye', #'',
2023                    ]
2024    return [prm for prm in parmList if prm.split(':')[2] not in NonRefinedList]
2025       
2026def getDescr(name):
2027    '''Return a short description for a GSAS-II variable
2028
2029    :param str name: The descriptive part of the variable name without colons (:)
2030
2031    :returns: a short description or None if not found
2032    '''
2033
2034    CompileVarDesc() # compile the regular expressions, if needed
2035    for key in reVarDesc:
2036        m = key.match(name)
2037        if m:
2038            reVarDesc[key]
2039            return m.expand(reVarDesc[key])
2040    return None
2041
2042def getVarStep(name,parmDict=None):
2043    '''Return a step size for computing the derivative of a GSAS-II variable
2044
2045    :param str name: A complete variable name (with colons, :)
2046    :param dict parmDict: A dict with parameter values or None (default)
2047
2048    :returns: a float that should be an appropriate step size, either from
2049      the value supplied in :func:`CompileVarDesc` or based on the value for
2050      name in parmDict, if supplied. If not found or the value is zero,
2051      a default value of 1e-5 is used. If parmDict is None (default) and
2052      no value is provided in :func:`CompileVarDesc`, then None is returned.
2053    '''
2054    CompileVarDesc() # compile the regular expressions, if needed
2055    for key in reVarStep:
2056        m = key.match(name)
2057        if m:
2058            return reVarStep[key]
2059    if parmDict is None: return None
2060    val = parmDict.get(key,0.0)
2061    if abs(val) > 0.05:
2062        return abs(val)/1000.
2063    else:
2064        return 1e-5
2065
2066def GenWildCard(varlist):
2067    '''Generate wildcard versions of G2 variables. These introduce '*'
2068    for a phase, histogram or atom number (but only for one of these
2069    fields) but only when there is more than one matching variable in the
2070    input variable list. So if the input is this::
2071
2072      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
2073
2074    then the output will be this::
2075
2076       wildList = ['*::AUiso:0', '0::AUiso:*']
2077
2078    :param list varlist: an input list of GSAS-II variable names
2079      (such as 0::AUiso:0)
2080
2081    :returns: wildList, the generated list of wild card variable names.
2082    '''
2083    wild = []
2084    for i in (0,1,3):
2085        currentL = varlist[:]
2086        while currentL:
2087            item1 = currentL.pop(0)
2088            i1splt = item1.split(':')
2089            if i >= len(i1splt): continue
2090            if i1splt[i]:
2091                nextL = []
2092                i1splt[i] = '[0-9]+'
2093                rexp = re.compile(':'.join(i1splt))
2094                matchlist = [item1]
2095                for nxtitem in currentL:
2096                    if rexp.match(nxtitem):
2097                        matchlist += [nxtitem]
2098                    else:
2099                        nextL.append(nxtitem)
2100                if len(matchlist) > 1:
2101                    i1splt[i] = '*'
2102                    wild.append(':'.join(i1splt))
2103                currentL = nextL
2104    return wild
2105
2106def LookupWildCard(varname,varlist):
2107    '''returns a list of variable names from list varname
2108    that match wildcard name in varname
2109
2110    :param str varname: a G2 variable name containing a wildcard
2111      (such as \\*::var)
2112    :param list varlist: the list of all variable names used in
2113      the current project
2114    :returns: a list of matching GSAS-II variables (may be empty)
2115    '''
2116    rexp = re.compile(varname.replace('*','[0-9]+'))
2117    return sorted([var for var in varlist if rexp.match(var)])
2118
2119def prmLookup(name,prmDict):
2120    '''Looks for a parameter in a min/max dictionary, optionally
2121    considering a wild card for histogram or atom number (use of
2122    both will never occur at the same time).
2123
2124    :param name: a GSAS-II parameter name (str, see :func:`getVarDescr`
2125      and :func:`CompileVarDesc`) or a :class:`G2VarObj` object.
2126    :param dict prmDict: a min/max dictionary, (parmMinDict
2127      or parmMaxDict in Controls) where keys are :class:`G2VarObj`
2128      objects.
2129    :returns: Two values, (**matchname**, **value**), are returned where:
2130
2131       * **matchname** *(str)* is the :class:`G2VarObj` object
2132         corresponding to the actual matched name,
2133         which could contain a wildcard even if **name** does not; and
2134       * **value** *(float)* which contains the parameter limit.
2135    '''
2136    for key,value in prmDict.items():
2137        if str(key) == str(name): return key,value
2138        if key == name: return key,value
2139    return None,None
2140       
2141
2142def _lookup(dic,key):
2143    '''Lookup a key in a dictionary, where None returns an empty string
2144    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
2145    '''
2146    if key is None:
2147        return ""
2148    elif key == "*":
2149        return "*"
2150    else:
2151        return dic.get(key,'?')
2152
2153def SortVariables(varlist):
2154    '''Sorts variable names in a sensible manner
2155    '''
2156    def cvnnums(var):
2157        v = []
2158        for i in var.split(':'):
2159            if i == '':
2160                v.append(-1)
2161                continue
2162            try:
2163                v.append(int(i))
2164            except:
2165                v.append(i)
2166        return v
2167    return sorted(varlist,key=cvnnums)
2168
2169class G2VarObj(object):
2170    '''Defines a GSAS-II variable either using the phase/atom/histogram
2171    unique Id numbers or using a character string that specifies
2172    variables by phase/atom/histogram number (which can change).
2173    Note that :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`,
2174    which calls :func:`IndexAllIds` (or
2175    :func:`GSASIIscriptable.G2Project.index_ids`) should be used to
2176    (re)load the current Ids
2177    before creating or later using the G2VarObj object.
2178
2179    This can store rigid body variables, but does not translate the residue # and
2180    body # to/from random Ids
2181
2182    A :class:`G2VarObj` object can be created with a single parameter:
2183
2184    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
2185      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
2186
2187     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
2188     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
2189     * a is the atom number (which may be left blank in which case the third colon is omitted).
2190       The atom number can be specified as '*' if a phase number is specified (not as '*').
2191       For rigid body variables, specify a will be a string of form "residue:body#"
2192
2193      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
2194      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
2195      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
2196      For a rigid body variables, AtomID is a string of form "residue:body#".
2197
2198    If four positional arguments are supplied, they are:
2199
2200    :param str/int phasenum: The number for the phase (or None or '*')
2201    :param str/int histnum: The number for the histogram (or None or '*')
2202    :param str varname: a single value can be used to create a :class:`G2VarObj`
2203    :param str/int atomnum: The number for the atom (or None or '*')
2204
2205    '''
2206    IDdict = {}
2207    IDdict['phases'] = {}
2208    IDdict['hists'] = {}
2209    IDdict['atoms'] = {}
2210    def __init__(self,*args):
2211        self.phase = None
2212        self.histogram = None
2213        self.name = ''
2214        self.atom = None
2215        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
2216            # single arg with 4 values
2217            self.phase,self.histogram,self.name,self.atom = args[0]
2218        elif len(args) == 1 and ':' in args[0]:
2219            #parse a string
2220            lst = args[0].split(':')
2221            if lst[0] == '*':
2222                self.phase = '*'
2223                if len(lst) > 3:
2224                    self.atom = lst[3]
2225                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2226            elif lst[1] == '*':
2227                self.histogram = '*'
2228                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2229            else:
2230                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2231                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2232                if len(lst) == 4:
2233                    if lst[3] == '*':
2234                        self.atom = '*'
2235                    else:
2236                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
2237                elif len(lst) == 5:
2238                    self.atom = lst[3]+":"+lst[4]
2239                elif len(lst) == 3:
2240                    pass
2241                else:
2242                    raise Exception("Too many colons in var name "+str(args[0]))
2243            self.name = lst[2]
2244        elif len(args) == 4:
2245            if args[0] == '*':
2246                self.phase = '*'
2247                self.atom = args[3]
2248            else:
2249                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
2250                if args[3] == '*':
2251                    self.atom = '*'
2252                elif args[0] is not None:
2253                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
2254            if args[1] == '*':
2255                self.histogram = '*'
2256            else:
2257                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
2258            self.name = args[2]
2259        else:
2260            raise Exception("Incorrectly called GSAS-II parameter name")
2261
2262        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
2263
2264    def __str__(self):
2265        return self.varname()
2266
2267    def __hash__(self):
2268        'Allow G2VarObj to be a dict key by implementing hashing'
2269        return hash(self.varname())
2270
2271    def varname(self):
2272        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
2273        string (p:h:<var>:a) or (p:h:<var>)
2274
2275        :returns: the variable name as a str
2276        '''
2277        a = ""
2278        if self.phase == "*":
2279            ph = "*"
2280            if self.atom:
2281                a = ":" + str(self.atom)
2282        else:
2283            ph = _lookup(PhaseRanIdLookup,self.phase)
2284            if self.atom == '*':
2285                a = ':*'
2286            elif self.atom:
2287                if ":" in str(self.atom):
2288                    a = ":" + str(self.atom)
2289                elif ph in AtomRanIdLookup:
2290                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
2291                else:
2292                    a = ":?"
2293        if self.histogram == "*":
2294            hist = "*"
2295        else:
2296            hist = _lookup(HistRanIdLookup,self.histogram)
2297        s = (ph + ":" + hist + ":" + str(self.name)) + a
2298        return s
2299
2300    def __repr__(self):
2301        '''Return the detailed contents of the object
2302        '''
2303        s = "<"
2304        if self.phase == '*':
2305            s += "Phases: all; "
2306            if self.atom is not None:
2307                if ":" in str(self.atom):
2308                    s += "Rigid body" + str(self.atom) + "; "
2309                else:
2310                    s += "Atom #" + str(self.atom) + "; "
2311        elif self.phase is not None:
2312            ph =  _lookup(PhaseRanIdLookup,self.phase)
2313            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
2314            if self.atom == '*':
2315                s += "Atoms: all; "
2316            elif ":" in str(self.atom):
2317                s += "Rigid body" + str(self.atom) + "; "
2318            elif self.atom is not None:
2319                s += "Atom rId=" + str(self.atom)
2320                if ph in AtomRanIdLookup:
2321                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
2322                else:
2323                    s += " (#? -- not found!); "
2324        if self.histogram == '*':
2325            s += "Histograms: all; "
2326        elif self.histogram is not None:
2327            hist = _lookup(HistRanIdLookup,self.histogram)
2328            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
2329        s += 'Variable name="' + str(self.name) + '">'
2330        return s+" ("+self.varname()+")"
2331
2332    def __eq__(self, other):
2333        '''Allow comparison of G2VarObj to other G2VarObj objects or strings.
2334        If any field is a wildcard ('*') that field matches.
2335        '''
2336        if type(other) is str:
2337            other = G2VarObj(other)
2338        elif type(other) is not G2VarObj:
2339            raise Exception("Invalid type ({}) for G2VarObj comparison with {}"
2340                            .format(type(other),other))
2341        if self.phase != other.phase and self.phase != '*' and other.phase != '*':
2342            return False
2343        if self.histogram != other.histogram and self.histogram != '*' and other.histogram != '*':
2344            return False
2345        if self.atom != other.atom and self.atom != '*' and other.atom != '*':
2346            return False
2347        if self.name != other.name:
2348            return False
2349        return True
2350
2351    def _show(self):
2352        'For testing, shows the current lookup table'
2353        print ('phases'+ self.IDdict['phases'])
2354        print ('hists'+ self.IDdict['hists'])
2355        print ('atomDict'+ self.IDdict['atoms'])
2356
2357#==========================================================================
2358def SetDefaultSample():
2359    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
2360    return {
2361        'InstrName':'',
2362        'ranId':ran.randint(0,sys.maxsize),
2363        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
2364        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],
2365        'Temperature':300.,'Pressure':0.1,'Time':0.0,
2366        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
2367        'Gonio. radius':200.0,
2368        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
2369#SASD items
2370        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
2371        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
2372        'Trans':1.0,                            #measured transmission
2373        'SlitLen':0.0,                          #Slit length - in Q(A-1)
2374        }
2375######################################################################
2376class ImportBaseclass(object):
2377    '''Defines a base class for the reading of input files (diffraction
2378    data, coordinates,...). See :ref:`Writing a Import Routine<import_routines>`
2379    for an explanation on how to use a subclass of this class.
2380    '''
2381    class ImportException(Exception):
2382        '''Defines an Exception that is used when an import routine hits an expected error,
2383        usually in .Reader.
2384
2385        Good practice is that the Reader should define a value in self.errors that
2386        tells the user some information about what is wrong with their file.
2387        '''
2388        pass
2389
2390    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
2391    def __init__(self,formatName,longFormatName=None,
2392                 extensionlist=[],strictExtension=False,):
2393        self.formatName = formatName # short string naming file type
2394        if longFormatName: # longer string naming file type
2395            self.longFormatName = longFormatName
2396        else:
2397            self.longFormatName = formatName
2398        # define extensions that are allowed for the file type
2399        # for windows, remove any extensions that are duplicate, as case is ignored
2400        if sys.platform == 'windows' and extensionlist:
2401            extensionlist = list(set([s.lower() for s in extensionlist]))
2402        self.extensionlist = extensionlist
2403        # If strictExtension is True, the file will not be read, unless
2404        # the extension matches one in the extensionlist
2405        self.strictExtension = strictExtension
2406        self.errors = ''
2407        self.warnings = ''
2408        self.SciPy = False          #image reader needed scipy
2409        # used for readers that will use multiple passes to read
2410        # more than one data block
2411        self.repeat = False
2412        self.selections = []
2413        self.repeatcount = 0
2414        self.readfilename = '?'
2415        self.scriptable = False
2416        #print 'created',self.__class__
2417
2418    def ReInitialize(self):
2419        'Reinitialize the Reader to initial settings'
2420        self.errors = ''
2421        self.warnings = ''
2422        self.SciPy = False          #image reader needed scipy
2423        self.repeat = False
2424        self.repeatcount = 0
2425        self.readfilename = '?'
2426
2427
2428#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
2429#        '''This method must be supplied in the child class to read the file.
2430#        if the read fails either return False or raise an Exception
2431#        preferably of type ImportException.
2432#        '''
2433#        #start reading
2434#        raise ImportException("Error occurred while...")
2435#        self.errors += "Hint for user on why the error occur
2436#        return False # if an error occurs
2437#        return True # if read OK
2438
2439    def ExtensionValidator(self, filename):
2440        '''This methods checks if the file has the correct extension
2441       
2442        :returns:
2443       
2444          * False if this filename will not be supported by this reader (only
2445            when strictExtension is True)
2446          * True if the extension matches the list supplied by the reader
2447          * None if the reader allows un-registered extensions
2448         
2449        '''
2450        if filename:
2451            ext = ospath.splitext(filename)[1]
2452            if not ext and self.strictExtension: return False
2453            for ext in self.extensionlist:               
2454                if sys.platform == 'windows':
2455                    if filename.lower().endswith(ext): return True
2456                else:
2457                    if filename.endswith(ext): return True
2458        if self.strictExtension:
2459            return False
2460        else:
2461            return None
2462
2463    def ContentsValidator(self, filename):
2464        '''This routine will attempt to determine if the file can be read
2465        with the current format.
2466        This will typically be overridden with a method that
2467        takes a quick scan of [some of]
2468        the file contents to do a "sanity" check if the file
2469        appears to match the selected format.
2470        the file must be opened here with the correct format (binary/text)
2471        '''
2472        #filepointer.seek(0) # rewind the file pointer
2473        return True
2474
2475    def CIFValidator(self, filepointer):
2476        '''A :meth:`ContentsValidator` for use to validate CIF files.
2477        '''
2478        filepointer.seek(0)
2479        for i,l in enumerate(filepointer):
2480            if i >= 1000: return True
2481            '''Encountered only blank lines or comments in first 1000
2482            lines. This is unlikely, but assume it is CIF anyway, since we are
2483            even less likely to find a file with nothing but hashes and
2484            blank lines'''
2485            line = l.strip()
2486            if len(line) == 0: # ignore blank lines
2487                continue
2488            elif line.startswith('#'): # ignore comments
2489                continue
2490            elif line.startswith('data_'): # on the right track, accept this file
2491                return True
2492            else: # found something invalid
2493                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
2494                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
2495                    self.errors += '  '+str(l)
2496                else:
2497                    self.errors += '  (binary)'
2498                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
2499                self.errors += '\n        a data_ statement begins a block.'
2500                return False
2501
2502######################################################################
2503class ImportPhase(ImportBaseclass):
2504    '''Defines a base class for the reading of files with coordinates
2505
2506    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
2507    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` and in
2508    :func:`GSASIIscriptable.import_generic`.
2509    See :ref:`Writing a Import Routine<import_routines>`
2510    for an explanation on how to use this class.
2511
2512    '''
2513    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2514        strictExtension=False,):
2515        # call parent __init__
2516        ImportBaseclass.__init__(self,formatName,longFormatName,
2517            extensionlist,strictExtension)
2518        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
2519        self.SymOps = {} # specified when symmetry ops are in file (e.g. CIF)
2520        self.Constraints = None
2521
2522######################################################################
2523class ImportStructFactor(ImportBaseclass):
2524    '''Defines a base class for the reading of files with tables
2525    of structure factors.
2526
2527    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
2528    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
2529    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2530    :meth:`Reader`.
2531
2532    See :ref:`Writing a Import Routine<import_routines>`
2533    for an explanation on how to use import classes in general. The specifics
2534    for reading a structure factor histogram require that
2535    the ``Reader()`` routine in the import
2536    class need to do only a few things: It
2537    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2538    and set :attr:`Parameters` with the instrument parameters
2539    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2540    '''
2541    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2542        strictExtension=False,):
2543        ImportBaseclass.__init__(self,formatName,longFormatName,
2544            extensionlist,strictExtension)
2545
2546        # define contents of Structure Factor entry
2547        self.Parameters = []
2548        'self.Parameters is a list with two dicts for data parameter settings'
2549        self.InitParameters()
2550        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2551        self.Banks = []             #for multi bank data (usually TOF)
2552        '''self.RefDict is a dict containing the reflection information, as read from the file.
2553        Item 'RefList' contains the reflection information. See the
2554        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
2555        for the contents of each row. Dict element 'FF'
2556        contains the form factor values for each element type; if this entry
2557        is left as initialized (an empty list) it will be initialized as needed later.
2558        '''
2559    def ReInitialize(self):
2560        'Reinitialize the Reader to initial settings'
2561        ImportBaseclass.ReInitialize(self)
2562        self.InitParameters()
2563        self.Banks = []             #for multi bank data (usually TOF)
2564        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2565
2566    def InitParameters(self):
2567        'initialize the instrument parameters structure'
2568        Lambda = 0.70926
2569        HistType = 'SXC'
2570        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2571                            'Lam':[Lambda,Lambda]
2572                            }, {}]
2573        'Parameters is a list with two dicts for data parameter settings'
2574
2575    def UpdateParameters(self,Type=None,Wave=None):
2576        'Revise the instrument parameters'
2577        if Type is not None:
2578            self.Parameters[0]['Type'] = [Type,Type]
2579        if Wave is not None:
2580            self.Parameters[0]['Lam'] = [Wave,Wave]
2581
2582######################################################################
2583class ImportPowderData(ImportBaseclass):
2584    '''Defines a base class for the reading of files with powder data.
2585
2586    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2587    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder` and in
2588    :func:`GSASIIscriptable.import_generic`.
2589    See :ref:`Writing a Import Routine<import_routines>`
2590    for an explanation on how to use this class.
2591    '''
2592    def __init__(self,formatName,longFormatName=None,
2593        extensionlist=[],strictExtension=False,):
2594        ImportBaseclass.__init__(self,formatName,longFormatName,
2595            extensionlist,strictExtension)
2596        self.clockWd = None  # used in TOF
2597        self.ReInitialize()
2598
2599    def ReInitialize(self):
2600        'Reinitialize the Reader to initial settings'
2601        ImportBaseclass.ReInitialize(self)
2602        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2603        self.powderdata = [] # Powder dataset
2604        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2605                np.array(x), # x-axis values
2606                np.array(y), # powder pattern intensities
2607                np.array(w), # 1/sig(intensity)^2 values (weights)
2608                np.array(yc), # calc. intensities (zero)
2609                np.array(yb), # calc. background (zero)
2610                np.array(yd), # obs-calc profiles
2611        '''
2612        self.comments = []
2613        self.idstring = ''
2614        self.Sample = SetDefaultSample() # default sample parameters
2615        self.Controls = {}  # items to be placed in top-level Controls
2616        self.GSAS = None     # used in TOF
2617        self.repeat_instparm = True # Should a parm file be
2618        #                             used for multiple histograms?
2619        self.instparm = None # name hint from file of instparm to use
2620        self.instfile = '' # full path name to instrument parameter file
2621        self.instbank = '' # inst parm bank number
2622        self.instmsg = ''  # a label that gets printed to show
2623                           # where instrument parameters are from
2624        self.numbanks = 1
2625        self.instdict = {} # place items here that will be transferred to the instrument parameters
2626        self.pwdparms = {} # place parameters that are transferred directly to the tree
2627                           # here (typically from an existing GPX file)
2628######################################################################
2629class ImportSmallAngleData(ImportBaseclass):
2630    '''Defines a base class for the reading of files with small angle data.
2631    See :ref:`Writing a Import Routine<import_routines>`
2632    for an explanation on how to use this class.
2633    '''
2634    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2635        strictExtension=False,):
2636
2637        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2638            strictExtension)
2639        self.ReInitialize()
2640
2641    def ReInitialize(self):
2642        'Reinitialize the Reader to initial settings'
2643        ImportBaseclass.ReInitialize(self)
2644        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2645        self.smallangledata = [] # SASD dataset
2646        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2647                np.array(x), # x-axis values
2648                np.array(y), # powder pattern intensities
2649                np.array(w), # 1/sig(intensity)^2 values (weights)
2650                np.array(yc), # calc. intensities (zero)
2651                np.array(yd), # obs-calc profiles
2652                np.array(yb), # preset bkg
2653        '''
2654        self.comments = []
2655        self.idstring = ''
2656        self.Sample = SetDefaultSample()
2657        self.GSAS = None     # used in TOF
2658        self.clockWd = None  # used in TOF
2659        self.numbanks = 1
2660        self.instdict = {} # place items here that will be transferred to the instrument parameters
2661
2662######################################################################
2663class ImportReflectometryData(ImportBaseclass):
2664    '''Defines a base class for the reading of files with reflectometry data.
2665    See :ref:`Writing a Import Routine<import_routines>`
2666    for an explanation on how to use this class.
2667    '''
2668    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2669        strictExtension=False,):
2670
2671        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2672            strictExtension)
2673        self.ReInitialize()
2674
2675    def ReInitialize(self):
2676        'Reinitialize the Reader to initial settings'
2677        ImportBaseclass.ReInitialize(self)
2678        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2679        self.reflectometrydata = [] # SASD dataset
2680        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2681                np.array(x), # x-axis values
2682                np.array(y), # powder pattern intensities
2683                np.array(w), # 1/sig(intensity)^2 values (weights)
2684                np.array(yc), # calc. intensities (zero)
2685                np.array(yd), # obs-calc profiles
2686                np.array(yb), # preset bkg
2687        '''
2688        self.comments = []
2689        self.idstring = ''
2690        self.Sample = SetDefaultSample()
2691        self.GSAS = None     # used in TOF
2692        self.clockWd = None  # used in TOF
2693        self.numbanks = 1
2694        self.instdict = {} # place items here that will be transferred to the instrument parameters
2695
2696######################################################################
2697class ImportPDFData(ImportBaseclass):
2698    '''Defines a base class for the reading of files with PDF G(R) data.
2699    See :ref:`Writing a Import Routine<import_routines>`
2700    for an explanation on how to use this class.
2701    '''
2702    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2703        strictExtension=False,):
2704
2705        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2706            strictExtension)
2707        self.ReInitialize()
2708
2709    def ReInitialize(self):
2710        'Reinitialize the Reader to initial settings'
2711        ImportBaseclass.ReInitialize(self)
2712        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2713        self.pdfdata = [] # PDF G(R) dataset
2714        '''A pdf g(r) data set is a list with items [x,y]:
2715                np.array(x), # r-axis values
2716                np.array(y), # pdf g(r)
2717        '''
2718        self.comments = []
2719        self.idstring = ''
2720        self.numbanks = 1
2721
2722######################################################################
2723class ImportImage(ImportBaseclass):
2724    '''Defines a base class for the reading of images
2725
2726    Images are read in only these places:
2727
2728      * Initial reading is typically done from a menu item
2729        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2730        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2731        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2732        :meth:`Reader`. This returns a list of reader objects for each read image.
2733        Also used in :func:`GSASIIscriptable.import_generic`.
2734
2735      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2736        directly into the data tree.
2737
2738      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2739
2740    When reading an image, the ``Reader()`` routine in the ImportImage class
2741    should set:
2742
2743      * :attr:`Comments`: a list of strings (str),
2744      * :attr:`Npix`: the number of pixels in the image (int),
2745      * :attr:`Image`: the actual image as a numpy array (np.array)
2746      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2747        data items are needed:
2748
2749         * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2750         * 'wavelength': wavelength in :math:`\\AA`.
2751         * 'distance': distance of detector from sample in cm.
2752         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2753         * 'size': size of image (such as ``[2048,2048]``).
2754         * 'ImageTag': image number or other keyword used to retrieve image from
2755           a multi-image data file (defaults to ``1`` if not specified).
2756         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2757
2758    optional data items:
2759
2760      * :attr:`repeat`: set to True if there are additional images to
2761        read in the file, False otherwise
2762      * :attr:`repeatcount`: set to the number of the image.
2763
2764    Note that the above is initialized with :meth:`InitParameters`.
2765    (Also see :ref:`Writing a Import Routine<import_routines>`
2766    for an explanation on how to use import classes in general.)
2767    '''
2768    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2769        strictExtension=False,):
2770        ImportBaseclass.__init__(self,formatName,longFormatName,
2771            extensionlist,strictExtension)
2772        self.InitParameters()
2773
2774    def ReInitialize(self):
2775        'Reinitialize the Reader to initial settings -- not used at present'
2776        ImportBaseclass.ReInitialize(self)
2777        self.InitParameters()
2778
2779    def InitParameters(self):
2780        'initialize the instrument parameters structure'
2781        self.Comments = ['No comments']
2782        self.Data = {}
2783        self.Npix = 0
2784        self.Image = None
2785        self.repeat = False
2786        self.repeatcount = 1
2787        self.sumfile = ''
2788
2789    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2790        '''Optionally, call this after reading in an image to load it into the tree.
2791        This saves time by preventing a reread of the same information.
2792        '''
2793        if ParentFrame:
2794            ParentFrame.ImageZ = self.Image   # store the image for plotting
2795            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2796            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2797
2798#################################################################################################
2799# shortcut routines
2800exp = np.exp
2801sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2802cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2803tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2804sqrt = sq = lambda x: np.sqrt(x)
2805pi = lambda: np.pi
2806
2807def FindFunction(f):
2808    '''Find the object corresponding to function f
2809
2810    :param str f: a function name such as 'numpy.exp'
2811    :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2812      that defines the package location(s) and where pkgobj
2813      defines the object associated with the function.
2814      If the function is not found, pkgobj is None.
2815    '''
2816    df = f.split('.')
2817    pkgdict = {}
2818    # no listed module name, try in current namespace
2819    if len(df) == 1:
2820        try:
2821            fxnobj = eval(f)
2822            return pkgdict,fxnobj
2823        except (AttributeError, NameError):
2824            return None,None
2825
2826    # includes a package, see if package is already imported
2827    pkgnam = '.'.join(df[:-1])
2828    try:
2829        fxnobj = eval(f)
2830        pkgdict[pkgnam] = eval(pkgnam)
2831        return pkgdict,fxnobj
2832    except (AttributeError, NameError):
2833        pass
2834    # package not yet imported, so let's try
2835    if '.' not in sys.path: sys.path.append('.')
2836    pkgnam = '.'.join(df[:-1])
2837    #for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2838    #    if pkgname:
2839    #        pkgname += '.' + pkg
2840    #    else:
2841    #        pkgname = pkg
2842    try:
2843        exec('import '+pkgnam)
2844        pkgdict[pkgnam] = eval(pkgnam)
2845        fxnobj = eval(f)
2846    except Exception as msg:
2847        print('load of '+pkgnam+' failed with error='+str(msg))
2848        return {},None
2849    # can we access the function? I am not exactly sure what
2850    #    I intended this to test originally (BHT)
2851    try:
2852        fxnobj = eval(f,globals(),pkgdict)
2853        return pkgdict,fxnobj
2854    except Exception as msg:
2855        print('call to',f,' failed with error=',str(msg))
2856        return None,None # not found
2857               
2858class ExpressionObj(object):
2859    '''Defines an object with a user-defined expression, to be used for
2860    secondary fits or restraints. Object is created null, but is changed
2861    using :meth:`LoadExpression`. This contains only the minimum
2862    information that needs to be stored to save and load the expression
2863    and how it is mapped to GSAS-II variables.
2864    '''
2865    def __init__(self):
2866        self.expression = ''
2867        'The expression as a text string'
2868        self.assgnVars = {}
2869        '''A dict where keys are label names in the expression mapping to a GSAS-II
2870        variable. The value a G2 variable name.
2871        Note that the G2 variable name may contain a wild-card and correspond to
2872        multiple values.
2873        '''
2874        self.freeVars = {}
2875        '''A dict where keys are label names in the expression mapping to a free
2876        parameter. The value is a list with:
2877
2878         * a name assigned to the parameter
2879         * a value for to the parameter and
2880         * a flag to determine if the variable is refined.
2881        '''
2882        self.depVar = None
2883
2884        self.lastError = ('','')
2885        '''Shows last encountered error in processing expression
2886        (list of 1-3 str values)'''
2887
2888        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2889        self.distance_atoms = None  # to be used for defining atom distances
2890
2891    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2892        '''Load the expression and associated settings into the object. Raises
2893        an exception if the expression is not parsed, if not all functions
2894        are defined or if not all needed parameter labels in the expression
2895        are defined.
2896
2897        This will not test if the variable referenced in these definitions
2898        are actually in the parameter dictionary. This is checked when the
2899        computation for the expression is done in :meth:`SetupCalc`.
2900
2901        :param str expr: the expression
2902        :param list exprVarLst: parameter labels found in the expression
2903        :param dict varSelect: this will be 0 for Free parameters
2904          and non-zero for expression labels linked to G2 variables.
2905        :param dict varName: Defines a name (str) associated with each free parameter
2906        :param dict varValue: Defines a value (float) associated with each free parameter
2907        :param dict varRefflag: Defines a refinement flag (bool)
2908          associated with each free parameter
2909        '''
2910        self.expression = expr
2911        self.compiledExpr = None
2912        self.freeVars = {}
2913        self.assgnVars = {}
2914        for v in exprVarLst:
2915            if varSelect[v] == 0:
2916                self.freeVars[v] = [
2917                    varName.get(v),
2918                    varValue.get(v),
2919                    varRefflag.get(v),
2920                    ]
2921            else:
2922                self.assgnVars[v] = varName[v]
2923        self.CheckVars()
2924
2925    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2926        '''Load the expression and associated settings from the object into
2927        arrays used for editing.
2928
2929        :param list exprVarLst: parameter labels found in the expression
2930        :param dict varSelect: this will be 0 for Free parameters
2931          and non-zero for expression labels linked to G2 variables.
2932        :param dict varName: Defines a name (str) associated with each free parameter
2933        :param dict varValue: Defines a value (float) associated with each free parameter
2934        :param dict varRefflag: Defines a refinement flag (bool)
2935          associated with each free parameter
2936
2937        :returns: the expression as a str
2938        '''
2939        for v in self.freeVars:
2940            varSelect[v] = 0
2941            varName[v] = self.freeVars[v][0]
2942            varValue[v] = self.freeVars[v][1]
2943            varRefflag[v] = self.freeVars[v][2]
2944        for v in self.assgnVars:
2945            varSelect[v] = 1
2946            varName[v] = self.assgnVars[v]
2947        return self.expression
2948
2949    def GetVaried(self):
2950        'Returns the names of the free parameters that will be refined'
2951        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
2952
2953    def GetVariedVarVal(self):
2954        'Returns the names and values of the free parameters that will be refined'
2955        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
2956
2957    def UpdateVariedVars(self,varyList,values):
2958        'Updates values for the free parameters (after a refinement); only updates refined vars'
2959        for v in self.freeVars:
2960            if not self.freeVars[v][2]: continue
2961            if "::"+self.freeVars[v][0] not in varyList: continue
2962            indx = list(varyList).index("::"+self.freeVars[v][0])
2963            self.freeVars[v][1] = values[indx]
2964
2965    def GetIndependentVars(self):
2966        'Returns the names of the required independent parameters used in expression'
2967        return [self.assgnVars[v] for v in self.assgnVars]
2968
2969    def CheckVars(self):
2970        '''Check that the expression can be parsed, all functions are
2971        defined and that input loaded into the object is internally
2972        consistent. If not an Exception is raised.
2973
2974        :returns: a dict with references to packages needed to
2975          find functions referenced in the expression.
2976        '''
2977        ret = self.ParseExpression(self.expression)
2978        if not ret:
2979            raise Exception("Expression parse error")
2980        exprLblList,fxnpkgdict = ret
2981        # check each var used in expression is defined
2982        defined = list(self.assgnVars.keys()) + list(self.freeVars.keys())
2983        notfound = []
2984        for var in exprLblList:
2985            if var not in defined:
2986                notfound.append(var)
2987        if notfound:
2988            msg = 'Not all variables defined'
2989            msg1 = 'The following variables were not defined: '
2990            msg2 = ''
2991            for var in notfound:
2992                if msg: msg += ', '
2993                msg += var
2994            self.lastError = (msg1,'  '+msg2)
2995            raise Exception(msg)
2996        return fxnpkgdict
2997
2998    def ParseExpression(self,expr):
2999        '''Parse an expression and return a dict of called functions and
3000        the variables used in the expression. Returns None in case an error
3001        is encountered. If packages are referenced in functions, they are loaded
3002        and the functions are looked up into the modules global
3003        workspace.
3004
3005        Note that no changes are made to the object other than
3006        saving an error message, so that this can be used for testing prior
3007        to the save.
3008
3009        :returns: a list of used variables
3010        '''
3011        self.lastError = ('','')
3012        import ast
3013        def ASTtransverse(node,fxn=False):
3014            '''Transverse a AST-parsed expresson, compiling a list of variables
3015            referenced in the expression. This routine is used recursively.
3016
3017            :returns: varlist,fxnlist where
3018              varlist is a list of referenced variable names and
3019              fxnlist is a list of used functions
3020            '''
3021            varlist = []
3022            fxnlist = []
3023            if isinstance(node, list):
3024                for b in node:
3025                    v,f = ASTtransverse(b,fxn)
3026                    varlist += v
3027                    fxnlist += f
3028            elif isinstance(node, ast.AST):
3029                for a, b in ast.iter_fields(node):
3030                    if isinstance(b, ast.AST):
3031                        if a == 'func':
3032                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
3033                            continue
3034                        v,f = ASTtransverse(b,fxn)
3035                        varlist += v
3036                        fxnlist += f
3037                    elif isinstance(b, list):
3038                        v,f = ASTtransverse(b,fxn)
3039                        varlist += v
3040                        fxnlist += f
3041                    elif node.__class__.__name__ == "Name":
3042                        varlist += [b]
3043                    elif fxn and node.__class__.__name__ == "Attribute":
3044                        varlist += [b]
3045            return varlist,fxnlist
3046        try:
3047            exprast = ast.parse(expr)
3048        except SyntaxError:
3049            s = ''
3050            import traceback
3051            for i in traceback.format_exc().splitlines()[-3:-1]:
3052                if s: s += "\n"
3053                s += str(i)
3054            self.lastError = ("Error parsing expression:",s)
3055            return
3056        # find the variables & functions
3057        v,f = ASTtransverse(exprast)
3058        varlist = sorted(list(set(v)))
3059        fxnlist = list(set(f))
3060        pkgdict = {}
3061        # check the functions are defined
3062        for fxn in fxnlist:
3063            fxndict,fxnobj = FindFunction(fxn)
3064            if not fxnobj:
3065                self.lastError = ("Error: Invalid function",fxn,
3066                                  "is not defined")
3067                return
3068            if not hasattr(fxnobj,'__call__'):
3069                self.lastError = ("Error: Not a function.",fxn,
3070                                  "cannot be called as a function")
3071                return
3072            pkgdict.update(fxndict)
3073        return varlist,pkgdict
3074
3075    def GetDepVar(self):
3076        'return the dependent variable, or None'
3077        return self.depVar
3078
3079    def SetDepVar(self,var):
3080        'Set the dependent variable, if used'
3081        self.depVar = var
3082#==========================================================================
3083class ExpressionCalcObj(object):
3084    '''An object used to evaluate an expression from a :class:`ExpressionObj`
3085    object.
3086
3087    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
3088      an expression string and mappings for the parameter labels in that object.
3089    '''
3090    def __init__(self,exprObj):
3091        self.eObj = exprObj
3092        'The expression and mappings; a :class:`ExpressionObj` object'
3093        self.compiledExpr = None
3094        'The expression as compiled byte-code'
3095        self.exprDict = {}
3096        '''dict that defines values for labels used in expression and packages
3097        referenced by functions
3098        '''
3099        self.lblLookup = {}
3100        '''Lookup table that specifies the expression label name that is
3101        tied to a particular GSAS-II parameters in the parmDict.
3102        '''
3103        self.fxnpkgdict = {}
3104        '''a dict with references to packages needed to
3105        find functions referenced in the expression.
3106        '''
3107        self.varLookup = {}
3108        '''Lookup table that specifies the GSAS-II variable(s)
3109        indexed by the expression label name. (Used for only for diagnostics
3110        not evaluation of expression.)
3111        '''
3112        self.su = None
3113        '''Standard error evaluation where supplied by the evaluator
3114        '''
3115        # Patch: for old-style expressions with a (now removed step size)
3116        if '2' in platform.python_version_tuple()[0]: 
3117            basestr = basestring
3118        else:
3119            basestr = str
3120        for v in self.eObj.assgnVars:
3121            if not isinstance(self.eObj.assgnVars[v], basestr):
3122                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
3123        self.parmDict = {}
3124        '''A copy of the parameter dictionary, for distance and angle computation
3125        '''
3126
3127    def SetupCalc(self,parmDict):
3128        '''Do all preparations to use the expression for computation.
3129        Adds the free parameter values to the parameter dict (parmDict).
3130        '''
3131        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3132            return
3133        self.fxnpkgdict = self.eObj.CheckVars()
3134        # all is OK, compile the expression
3135        self.compiledExpr = compile(self.eObj.expression,'','eval')
3136
3137        # look at first value in parmDict to determine its type
3138        parmsInList = True
3139        if '2' in platform.python_version_tuple()[0]: 
3140            basestr = basestring
3141        else:
3142            basestr = str
3143        for key in parmDict:
3144            val = parmDict[key]
3145            if isinstance(val, basestr):
3146                parmsInList = False
3147                break
3148            try: # check if values are in lists
3149                val = parmDict[key][0]
3150            except (TypeError,IndexError):
3151                parmsInList = False
3152            break
3153
3154        # set up the dicts needed to speed computations
3155        self.exprDict = {}
3156        self.lblLookup = {}
3157        self.varLookup = {}
3158        for v in self.eObj.freeVars:
3159            varname = self.eObj.freeVars[v][0]
3160            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
3161            self.lblLookup[varname] = v
3162            self.varLookup[v] = varname
3163            if parmsInList:
3164                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
3165            else:
3166                parmDict[varname] = self.eObj.freeVars[v][1]
3167            self.exprDict[v] = self.eObj.freeVars[v][1]
3168        for v in self.eObj.assgnVars:
3169            varname = self.eObj.assgnVars[v]
3170            if varname in parmDict:
3171                self.lblLookup[varname] = v
3172                self.varLookup[v] = varname
3173                if parmsInList:
3174                    self.exprDict[v] = parmDict[varname][0]
3175                else:
3176                    self.exprDict[v] = parmDict[varname]
3177            elif '*' in varname:
3178                varlist = LookupWildCard(varname,list(parmDict.keys()))
3179                if len(varlist) == 0:
3180                    raise Exception("No variables match "+str(v))
3181                for var in varlist:
3182                    self.lblLookup[var] = v
3183                if parmsInList:
3184                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
3185                else:
3186                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
3187                self.varLookup[v] = [var for var in varlist]
3188            else:
3189                self.exprDict[v] = None
3190#                raise Exception,"No value for variable "+str(v)
3191        self.exprDict.update(self.fxnpkgdict)
3192
3193    def UpdateVars(self,varList,valList):
3194        '''Update the dict for the expression with a set of values
3195        :param list varList: a list of variable names
3196        :param list valList: a list of corresponding values
3197        '''
3198        for var,val in zip(varList,valList):
3199            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
3200
3201    def UpdateDict(self,parmDict):
3202        '''Update the dict for the expression with values in a dict
3203        :param dict parmDict: a dict of values, items not in use are ignored
3204        '''
3205        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3206            self.parmDict = parmDict
3207            return
3208        for var in parmDict:
3209            if var in self.lblLookup:
3210                self.exprDict[self.lblLookup[var]] = parmDict[var]
3211
3212    def EvalExpression(self):
3213        '''Evaluate an expression. Note that the expression
3214        and mapping are taken from the :class:`ExpressionObj` expression object
3215        and the parameter values were specified in :meth:`SetupCalc`.
3216        :returns: a single value for the expression. If parameter
3217        values are arrays (for example, from wild-carded variable names),
3218        the sum of the resulting expression is returned.
3219
3220        For example, if the expression is ``'A*B'``,
3221        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
3222
3223        [0.5, 1, 0.5]
3224
3225        then the result will be ``4.0``.
3226        '''
3227        self.su = None
3228        if self.eObj.expression.startswith('Dist'):
3229#            GSASIIpath.IPyBreak()
3230            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
3231            return dist
3232        elif self.eObj.expression.startswith('Angle'):
3233            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
3234            return angle
3235        if self.compiledExpr is None:
3236            raise Exception("EvalExpression called before SetupCalc")
3237        try:
3238            val = eval(self.compiledExpr,globals(),self.exprDict)
3239        except TypeError:
3240            val = None
3241        if not np.isscalar(val):
3242            val = np.sum(val)
3243        return val
3244
3245class G2Exception(Exception):
3246    'A generic GSAS-II exception class'
3247    def __init__(self,msg):
3248        self.msg = msg
3249    def __str__(self):
3250        return repr(self.msg)
3251
3252class G2RefineCancel(Exception):
3253    'Raised when Cancel is pressed in a refinement dialog'
3254    def __init__(self,msg):
3255        self.msg = msg
3256    def __str__(self):
3257        return repr(self.msg)
3258   
3259def HowDidIgetHere(wherecalledonly=False):
3260    '''Show a traceback with calls that brought us to the current location.
3261    Used for debugging.
3262    '''
3263    import traceback
3264    if wherecalledonly:
3265        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
3266        print(i.strip().rstrip())
3267    else:
3268        print (70*'*')
3269        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
3270        print (70*'*')
3271
3272# Note that this is GUI code and should be moved at somepoint
3273def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
3274    '''Create and initialize a new set of PDF tree entries
3275
3276    :param Frame G2frame: main GSAS-II tree frame object
3277    :param str PWDRtree: name of PWDR to be used to create PDF item
3278    :param dict ElList: data structure with composition
3279    :param list Qlimits: Q limits to be used for computing the PDF
3280    :param float numAtm: no. atom in chemical formula
3281    :param float FltBkg: flat background value
3282    :param list PDFnames: previously used PDF names
3283
3284    :returns: the Id of the newly created PDF entry
3285    '''
3286    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
3287    if PDFname in PDFnames:
3288        print('Skipping, entry already exists: '+PDFname)
3289        return None
3290    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
3291    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
3292    Data = {
3293        'Sample':{'Name':PWDRtree,'Mult':1.0},
3294        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
3295        'Container':{'Name':'','Mult':-1.0,'Refine':False},
3296        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
3297        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
3298        'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
3299        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,'Rmin':1.0,
3300        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
3301    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
3302    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
3303        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
3304    return Id
3305#%%
3306class ShowTiming(object):
3307    '''An object to use for timing repeated sections of code.
3308
3309    Create the object with::
3310       tim0 = ShowTiming()
3311
3312    Tag sections of code to be timed with::
3313       tim0.start('start')
3314       tim0.start('in section 1')
3315       tim0.start('in section 2')
3316       
3317    etc. (Note that each section should have a unique label.)
3318
3319    After the last section, end timing with::
3320       tim0.end()
3321
3322    Show timing results with::
3323       tim0.show()
3324       
3325    '''
3326    def __init__(self):
3327        self.timeSum =  []
3328        self.timeStart = []
3329        self.label = []
3330        self.prev = None
3331    def start(self,label):
3332        import time
3333        if label in self.label:
3334            i = self.label.index(label)
3335            self.timeStart[i] = time.time()
3336        else:
3337            i = len(self.label)
3338            self.timeSum.append(0.0)
3339            self.timeStart.append(time.time())
3340            self.label.append(label)
3341        if self.prev is not None:
3342            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
3343        self.prev = i
3344    def end(self):
3345        import time
3346        if self.prev is not None:
3347            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
3348        self.prev = None
3349    def show(self):
3350        sumT = sum(self.timeSum)
3351        print('Timing results (total={:.2f} sec)'.format(sumT))
3352        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
3353            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
3354#%%
3355
3356def validateAtomDrawType(typ,generalData={}):
3357    '''Confirm that the selected Atom drawing type is valid for the current
3358    phase. If not, use 'vdW balls'. This is currently used only for setting a
3359    default when atoms are added to the atoms draw list.
3360    '''
3361    if typ in ('lines','vdW balls','sticks','balls & sticks','ellipsoids'):
3362        return typ
3363    # elif generalData.get('Type','') == 'macromolecular':
3364    #     if typ in ('backbone',):
3365    #         return typ
3366    return 'vdW balls'
3367
3368if __name__ == "__main__":
3369    # test variable descriptions
3370    for var in '0::Afrac:*',':1:Scale','1::dAx:0','::undefined':
3371        v = var.split(':')[2]
3372        print(var+':\t', getDescr(v),getVarStep(v))
3373    import sys; sys.exit()
3374    # test equation evaluation
3375    def showEQ(calcobj):
3376        print (50*'=')
3377        print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
3378        for v in sorted(calcobj.varLookup):
3379            print ("  "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
3380        # print '  Derivatives'
3381        # for v in calcobj.derivStep.keys():
3382        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
3383
3384    obj = ExpressionObj()
3385
3386    obj.expression = "A*np.exp(B)"
3387    obj.assgnVars =  {'B': '0::Afrac:1'}
3388    obj.freeVars =  {'A': [u'A', 0.5, True]}
3389    #obj.CheckVars()
3390    calcobj = ExpressionCalcObj(obj)
3391
3392    obj1 = ExpressionObj()
3393    obj1.expression = "A*np.exp(B)"
3394    obj1.assgnVars =  {'B': '0::Afrac:*'}
3395    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
3396    #obj.CheckVars()
3397    calcobj1 = ExpressionCalcObj(obj1)
3398
3399    obj2 = ExpressionObj()
3400    obj2.distance_stuff = np.array([[0,1],[1,-1]])
3401    obj2.expression = "Dist(1,2)"
3402    GSASIIpath.InvokeDebugOpts()
3403    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3404    calcobj2 = ExpressionCalcObj(obj2)
3405    calcobj2.SetupCalc(parmDict2)
3406    showEQ(calcobj2)
3407
3408    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
3409    print ('\nDict = '+parmDict1)
3410    calcobj.SetupCalc(parmDict1)
3411    showEQ(calcobj)
3412    calcobj1.SetupCalc(parmDict1)
3413    showEQ(calcobj1)
3414
3415    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3416    print ('Dict = '+parmDict2)
3417    calcobj.SetupCalc(parmDict2)
3418    showEQ(calcobj)
3419    calcobj1.SetupCalc(parmDict2)
3420    showEQ(calcobj1)
3421    calcobj2.SetupCalc(parmDict2)
3422    showEQ(calcobj2)
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