source: trunk/GSASIIobj.py @ 3597

Last change on this file since 3597 was 3597, checked in by vondreele, 4 years ago

fix spelling errors in the list of parameter manes

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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2018-09-13 17:35:37 +0000 (Thu, 13 Sep 2018) $
5# $Author: vondreele $
6# $Revision: 3597 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 3597 2018-09-13 17:35:37Z 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
18Constraints Tree Item
19----------------------
20
21.. _Constraints_table:
22
23.. index::
24   single: Constraints object description
25   single: Data object descriptions; Constraints
26
27Constraints are stored in a dict, separated into groups.
28Note that parameter are named in the following pattern,
29p:h:<var>:n, where p is the phase number, h is the histogram number
30<var> is a variable name and n is the parameter number.
31If a parameter does not depend on a histogram or phase or is unnumbered, that
32number is omitted.
33Note that the contents of each dict item is a List where each element in the
34list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
35The constraints in this form are converted in
36:func:`GSASIIstrIO.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
37
38The keys in the Constraints dict are:
39
40.. tabularcolumns:: |l|p{4.5in}|
41
42==========  ====================================================
43  key         explanation
44==========  ====================================================
45Hist        This specifies a list of constraints on
46            histogram-related parameters,
47            which will be of form :h:<var>:n.
48HAP         This specifies a list of constraints on parameters
49            that are defined for every histogram in each phase
50            and are of form p:h:<var>:n.
51Phase       This specifies a list of constraints on phase
52            parameters,
53            which will be of form p::<var>:n.
54Global      This specifies a list of constraints on parameters
55            that are not tied to a histogram or phase and
56            are of form ::<var>:n
57==========  ====================================================
58
59.. _Constraint_definitions_table:
60
61.. index::
62   single: Constraint definition object description
63   single: Data object descriptions; Constraint Definition
64
65Each constraint is defined as an item in a list. Each constraint is of form::
66
67[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
68
69Where the variable pair list item containing two values [<mult>, <var>], where:
70
71  * <mult> is a multiplier for the constraint (float)
72  * <var> a :class:`G2VarObj` object (previously a str variable name of form
73      'p:h:name[:at]')
74
75Note that the last three items in the list play a special role:
76
77 * <fixedval> is the fixed value for a `constant equation` (``constype=c``)
78   constraint or is None. For a `New variable` (``constype=f``) constraint,
79   a variable name can be specified as a str (used for externally
80   generated constraints)
81 * <varyflag> is True or False for `New variable` (``constype=f``) constraints
82   or is None. This will be implemented in the future to indicate if these variables
83   should be refined.
84 * <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
85
86    * 'e' defines a set of equivalent variables. Only the first variable is refined (if the
87      appropriate refine flag is set) and and all other equivalent variables in the list
88      are generated from that variable, using the appropriate multipliers.
89    * 'c' defines a constraint equation of form,
90      :math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
91    * 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
92      even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
93      constraint and the mult value is ignored.
94      This is of particular value when needing to hold one or more variables where a
95      single flag controls a set of variables such as, coordinates,
96      the reciprocal metric tensor or anisotropic displacement parameter.
97    * 'f' defines a new variable (function) according to relationship
98      :math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
99
100Covariance Tree Item
101--------------------
102
103.. _Covariance_table:
104
105.. index::
106   single: Covariance description
107   single: Data object descriptions; Covariance
108
109The Covariance tree item has results from the last least-squares run. They
110are stored in a dict with these keys:
111
112.. tabularcolumns:: |l|l|p{4in}|
113
114=============  ===============  ====================================================
115  key            sub-key        explanation
116=============  ===============  ====================================================
117newCellDict    \                dict with lattice parameters computed by
118                                :func:`GSASIIstrMath.GetNewCellParms` (dict)
119title          \                Name of gpx file(?) (str)
120variables      \                Values for all N refined variables
121                                (list of float values, length N,
122                                ordered to match varyList)
123sig            \                Uncertainty values for all N refined variables
124                                (list of float values, length N,
125                                ordered to match varyList)
126varyList       \                List of directly refined variables
127                                (list of str values, length N)
128newAtomDict    \                dict with atom position values computed in
129                                :func:`GSASIIstrMath.ApplyXYZshifts` (dict)
130Rvals          \                R-factors, GOF, Marquardt value for last
131                                refinement cycle (dict)
132\              Nobs             Number of observed data points (int)
133\              Rwp              overall weighted profile R-factor (%, float)
134\              chisq            sum[w*(Iobs-Icalc)**2] for all data
135                                note this is not the reduced chi squared (float)
136\              lamMax           Marquardt value applied to Hessian diagonal
137                                (float)
138\              GOF              The goodness-of-fit, aka square root of
139                                the reduced chi squared. (float)
140covMatrix      \                The (NxN) covVariance matrix (np.array)
141=============  ===============  ====================================================
142
143Phase Tree Items
144----------------
145
146.. _Phase_table:
147
148.. index::
149   single: Phase object description
150   single: Data object descriptions; Phase
151
152Phase information is stored in the GSAS-II data tree as children of the
153Phases item in a dict with keys:
154
155.. tabularcolumns:: |l|l|p{4in}|
156
157==========  ===============  ====================================================
158  key         sub-key        explanation
159==========  ===============  ====================================================
160General         \            Overall information for the phase (dict)
161  \         AtomPtrs         list of four locations to use to pull info
162                             from the atom records (list)
163  \         F000X            x-ray F(000) intensity (float)
164  \         F000N            neutron F(000) intensity (float)
165  \         Mydir            directory of current .gpx file (str)
166  \         MCSA controls    Monte Carlo-Simulated Annealing controls (dict)
167  \         Cell             List with 8 items: cell refinement flag (bool)
168                             a, b, c, (Angstrom, float)
169                             alpha, beta & gamma (degrees, float)
170                             volume (A^3, float)
171  \         Type             'nuclear' or 'macromolecular' for now (str)
172  \         Map              dict of map parameters
173  \         SH Texture       dict of spherical harmonic preferred orientation
174                             parameters
175  \         Isotope          dict of isotopes for each atom type
176  \         Isotopes         dict of scattering lengths for each isotope
177                             combination for each element in phase
178  \         Name             phase name (str)
179  \         SGData           Space group details as a :ref:`space group (SGData) object <SGData_table>`
180                             as defined in :func:`GSASIIspc.SpcGroup`.
181  \         Pawley neg wt    Restraint value for negative Pawley intensities
182                             (float)
183  \         Flip             dict of Charge flip controls
184  \         Data plot type   data plot type ('Mustrain', 'Size' or
185                             'Preferred orientation') for powder data (str)
186  \         Mass             Mass of unit cell contents in g/mol
187  \         POhkl            March-Dollase preferred orientation direction
188  \         Z                dict of atomic numbers for each atom type
189  \         vdWRadii         dict of van der Waals radii for each atom type
190  \         Color            Colors for atoms (list of (r,b,g) triplets)
191  \         AtomTypes        List of atom types
192  \         AtomMass         List of masses for atoms
193  \         doPawley         Flag for Pawley intensity extraction (bool)
194  \         NoAtoms          Number of atoms per unit cell of each type (dict)
195  \         Pawley dmin      maximum Q (as d-space) to use for Pawley
196                             extraction (float)
197  \         BondRadii        Default radius for each atom used to compute
198                             interatomic distances (list of floats)
199  \         AngleRadii       Default radius for each atom used to compute
200                             interatomic angles (list of floats)
201  \         DisAglCtls       Dict with distance/angle search controls,
202                             which has keys 'Name', 'AtomTypes',
203                             'BondRadii', 'AngleRadii' which are as above
204                             except are possibly edited. Also contains
205                             'Factors', which is a 2 element list with
206                             a multiplier for bond and angle search range
207                             [typically (0.85,0.85)].
208ranId           \            unique random number Id for phase (int)
209pId             \            Phase Id number for current project (int).
210Atoms           \            Atoms in phase as a list of lists. The outer list
211                             is for each atom, the inner list contains varying
212                             items depending on the type of phase, see
213                             the :ref:`Atom Records <Atoms_table>` description.
214                             (list of lists)
215Drawing         \            Display parameters (dict)
216\           ballScale        Size of spheres in ball-and-stick display (float)
217\           bondList         dict with bonds
218\           contourLevel     map contour level in e/A^3 (float)
219\           showABC          Flag to show view point triplet (bool). True=show.
220\           viewDir          cartesian viewing direction (np.array with three
221                             elements)
222\           Zclip            clipping distance in A (float)
223\           backColor        background for plot as and R,G,B triplet
224                             (default = [0, 0, 0], black).
225                             (list with three atoms)
226\           selectedAtoms    List of selected atoms (list of int values)
227\           showRigidBodies  Flag to highlight rigid body placement
228\           sizeH            Size ratio for H atoms (float)
229\           bondRadius       Size of binds in A (float)
230\           atomPtrs         positions of x, type, site sym, ADP flag in Draw Atoms (list)
231\           viewPoint        list of lists. First item in list is [x,y,z]
232                             in fractional coordinates for the center of
233                             the plot. Second item list of previous & current
234                             atom number viewed (may be [0,0])
235\           showHydrogen     Flag to control plotting of H atoms.
236\           unitCellBox      Flag to control display of the unit cell.
237\           ellipseProb      Probability limit for display of thermal
238                             ellipsoids in % (float).
239\           vdwScale         Multiplier of van der Waals radius for
240                             display of vdW spheres.
241\           Atoms            A list of lists with an entry for each atom
242                             that is plotted.
243\           Zstep            Step to de/increase Z-clip (float)
244\           Quaternion       Viewing quaternion (4 element np.array)
245\           radiusFactor     Distance ratio for searching for bonds. ? Bonds
246                             are located that are within r(Ra+Rb) and (Ra+Rb)/r
247                             where Ra and Rb are the atomic radii.
248\           oldxy            previous view point (list with two floats)
249\           cameraPos        Viewing position in A for plot (float)
250\           depthFog         True if use depthFog on plot - set currently as False (bool)
251RBModels        \            Rigid body assignments (note Rigid body definitions
252                             are stored in their own main top-level tree entry.)
253Pawley ref      \            Pawley reflections
254Histograms      \            A dict of dicts. The key for the outer dict is
255                             the histograms tied to this phase. The inner
256                             dict contains the combined phase/histogram
257                             parameters for items such as scale factors,
258                             size and strain parameters. The following are the
259                             keys to the inner dict. (dict)
260\           Babinet          For protein crystallography. Dictionary with two
261                             entries, 'BabA', 'BabU'
262\           Extinction       Extinction parameter (list of float, bool)
263\           HStrain          Hydrostatic strain. List of two lists. The first is
264                             a list of the HStrain parameters (1, 2, 3, 4, or 6
265                             depending on unit cell), the second is a list of boolean
266                             refinement parameters (same length)
267\           Histogram        The name of the associated histogram (str)
268\           LeBail           Flag for LeBail extraction (bool)
269\           Mustrain         List of microstrain parameters, in order:
270
271                               0. Type, one of u'generalized', u'isotropic',
272                                  u'uniaxial'
273                               1. Isotropic/uniaxial parameters - list of 3 floats
274                               2. Refinement flags - list of 3 bools
275                               3. Microstrain axis - list of 3 ints, [h, k, l]
276                               4. Generalized mustrain parameters - list of 2-6
277                                  floats, depending on space group
278                               5. Generalized refinement flags - list of bools,
279                                  corresponding to the parameters of (4)
280\           Pref.Ori.        Preferred Orientation. List of eight parameters.
281                             Items marked SH are only used for Spherical Harmonics.
282
283                               0. Type, 'MD' for March-Dollase or 'SH' for
284                                  Spherical Harmonics
285                               1. Value, float
286                               2. Refinement flag, bool
287                               3. Preferred direction, list of ints, [h, k, l]
288                               4. SH - number of terms, int
289                               5. SH - dict
290                               6. SH - list
291                               7. SH - float
292\           Scale            Phase fraction, list of [float, bool].
293\           Show             bool
294\           Use              bool
295\           newLeBail        Whether to perform a new LeBail extraction
296MCSA            \            Monte-Carlo simulated annealing parameters (dict)
297\
298==========  ===============  ====================================================
299
300Rigid Body Objects
301------------------
302
303.. _RBData_table:
304
305.. index::
306   single: Rigid Body Data description
307   single: Data object descriptions; Rigid Body Data
308
309Rigid body descriptions are available for two types of rigid bodies: 'Vector'
310and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
311with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
312with defined refinable torsion angles.
313
314.. tabularcolumns:: |l|l|p{4in}|
315
316==========  ===============  ====================================================
317  key         sub-key        explanation
318==========  ===============  ====================================================
319Vector      RBId             vector rigid bodies (dict of dict)
320\           AtInfo           Drad, Color: atom drawing radius & color for each atom type (dict)
321\           RBname           Name assigned by user to rigid body (str)
322\           VectMag          vector magnitudes in A (list)
323\           rbXYZ            Cartesian coordinates for Vector rigid body (list of 3 float)
324\           rbRef            3 assigned reference atom nos. in rigid body for origin
325                             definition, use center of atoms flag (list of 3 int & 1 bool)
326\           VectRef          refinement flags for VectMag values (list of bool)
327\           rbTypes          Atom types for each atom in rigid body (list of str)
328\           rbVect           Cartesian vectors for each translation used to build rigid body (list of lists)
329\           useCount         Number of times rigid body is used in any structure (int)
330Residue     RBId             residue rigid bodies (dict of dict)
331\           AtInfo           Drad, Color: atom drawing radius & color for each atom type(dict)
332\           RBname           Name assigned by user to rigid body (str)
333\           rbXYZ            Cartesian coordinates for Residue rigid body (list of 3 float)
334\           rbTypes          Atom types for each atom in rigid body (list of str)
335\           atNames          Names of each atom in rigid body (e.g. C1,N2...) (list of str)
336\           rbRef            3 assigned reference atom nos. in rigid body for origin
337                             definition, use center of atoms flag (list of 3 int & 1 bool)
338\           rbSeq            Orig,Piv,angle,Riding (list): definition of internal rigid body
339                             torsion; origin atom (int), pivot atom (int), torsion angle (float),
340                             riding atoms (list of int)
341\           SelSeq           [int,int] used by SeqSizer to identify objects
342\           useCount         Number of times rigid body is used in any structure (int)
343RBIds           \            unique Ids generated upon creation of each rigid body (dict)
344\           Vector           Ids for each Vector rigid body (list)
345\           Residue          Ids for each Residue rigid body (list)
346==========  ===============  ====================================================
347
348Space Group Objects
349-------------------
350
351.. _SGData_table:
352
353.. index::
354   single: Space Group Data description
355   single: Data object descriptions; Space Group Data
356
357Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
358and the information is placed in a SGdata object
359which is a dict with these keys:
360
361.. tabularcolumns:: |l|p{4.5in}|
362
363==========  ====================================================
364  key         explanation
365==========  ====================================================
366SpGrp       space group symbol (str)
367Laue        one of the following 14 Laue classes:
368            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
369            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
370SGInv       True if centrosymmetric, False if not (bool)
371SGLatt      Lattice centering type. Will be one of
372            P, A, B, C, I, F, R (str)
373SGUniq      unique axis if monoclinic. Will be
374            a, b, or c for monoclinic space groups.
375            Will be blank for non-monoclinic. (str)
376SGCen       Symmetry cell centering vectors. A (n,3) np.array
377            of centers. Will always have at least one row:
378            ``np.array([[0, 0, 0]])``
379SGOps       symmetry operations as a list of form
380            ``[[M1,T1], [M2,T2],...]``
381            where :math:`M_n` is a 3x3 np.array
382            and :math:`T_n` is a length 3 np.array.
383            Atom coordinates are transformed where the
384            Asymmetric unit coordinates [X is (x,y,z)]
385            are transformed using
386            :math:`X^\prime = M_n*X+T_n`
387SGSys       symmetry unit cell: type one of
388            'triclinic', 'monoclinic', 'orthorhombic',
389            'tetragonal', 'rhombohedral', 'trigonal',
390            'hexagonal', 'cubic' (str)
391SGPolax     Axes for space group polarity. Will be one of
392            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
393            'xyz'. In the case where axes are arbitrary
394            '111' is used (P 1, and ?).
395==========  ====================================================
396
397.. _SSGData_table:
398
399.. index::
400   single: Superspace Group Data description
401   single: Data object descriptions; Superspace Group Data
402
403Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
404and the information is placed in a SSGdata object
405which is a dict with these keys:
406
407.. tabularcolumns:: |l|p{4.5in}|
408
409==========  ====================================================
410  key         explanation
411==========  ====================================================
412SSpGrp      superspace group symbol extension to space group
413            symbol, accidental spaces removed
414SSGCen      4D cell centering vectors [0,0,0,0] at least
415SSGOps      4D symmetry operations as [M,T] so that M*x+T = x'
416==========  ====================================================
417
418
419Atom Records
420------------
421
422.. _Atoms_table:
423
424.. index::
425   single: Atoms record description
426   single: Data object descriptions; Atoms record
427
428
429If ``phasedict`` points to the phase information in the data tree, then
430atoms are contained in a list of atom records (list) in
431``phasedict['Atoms']``. Also needed to read atom information
432are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
433which define locations in the atom record, as shown below. Items shown are
434always present; additional ones for macromolecular phases are marked 'mm'
435
436.. tabularcolumns:: |l|p{4.5in}|
437
438==============   ====================================================
439location         explanation
440==============   ====================================================
441ct-4              mm - residue number (str)
442ct-3              mm - residue name (e.g. ALA) (str)
443ct-2              mm - chain label (str)
444ct-1              atom label (str)
445ct                atom type (str)
446ct+1              refinement flags; combination of 'F', 'X', 'U' (str)
447cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
448cx+3              site occupancy (float)
449cs                site symmetry (str)
450cs+1              site multiplicity (int)
451cia               ADP flag: Isotropic ('I') or Anisotropic ('A')
452cia+1             Uiso (float)
453cia+2...cia+7     U11, U22, U33, U12, U13, U23 (6 floats)
454atom[cia+8]       unique atom identifier (int)
455
456==============   ====================================================
457
458Drawing Atom Records
459--------------------
460
461.. _Drawing_atoms_table:
462
463.. index::
464   single: Drawing atoms record description
465   single: Data object descriptions; Drawing atoms record
466
467
468If ``phasedict`` points to the phase information in the data tree, then
469drawing atoms are contained in a list of drawing atom records (list) in
470``phasedict['Drawing']['Atoms']``. Also needed to read atom information
471are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
472which define locations in the atom record, as shown below. Items shown are
473always present; additional ones for macromolecular phases are marked 'mm'
474
475.. tabularcolumns:: |l|p{4.5in}|
476
477==============   ====================================================
478location         explanation
479==============   ====================================================
480ct-4              mm - residue number (str)
481ct-3              mm - residue name (e.g. ALA) (str)
482ct-2              mm - chain label (str)
483ct-1              atom label (str)
484ct                atom type (str)
485cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
486cs-1              Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str)
487cs                atom drawing style; e.g. 'balls & sticks' (str)
488cs+1              atom label style (e.g. 'name') (str)
489cs+2              atom color (RBG triplet) (int)
490cs+3              ADP flag: Isotropic ('I') or Anisotropic ('A')
491cs+4              Uiso (float)
492cs+5...cs+11      U11, U22, U33, U12, U13, U23 (6 floats)
493ci                unique atom identifier; matches source atom Id in Atom Records (int)
494==============   ====================================================
495
496Powder Diffraction Tree Items
497-----------------------------
498
499.. _Powder_table:
500
501.. index::
502   single: Powder data object description
503   single: Data object descriptions; Powder Data
504
505Every powder diffraction histogram is stored in the GSAS-II data tree
506with a top-level entry named beginning with the string "PWDR ". The
507diffraction data for that information are directly associated with
508that tree item and there are a series of children to that item. The
509routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
510and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
511load this information into a dictionary where the child tree name is
512used as a key, and the information in the main entry is assigned
513a key of ``Data``, as outlined below.
514
515.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
516
517======================  ===============  ====================================================
518  key                      sub-key        explanation
519======================  ===============  ====================================================
520Comments                      \           Text strings extracted from the original powder
521                                          data header. These cannot be changed by the user;
522                                          it may be empty.
523Limits                       \            A list of two two element lists, as [[Ld,Hd],[L,H]]
524                                          where L and Ld are the current and default lowest
525                                          two-theta value to be used and
526                                          where H and Hd are the current and default highest
527                                          two-theta value to be used.
528Reflection Lists              \           A dict with an entry for each phase in the
529                                          histogram. The contents of each dict item
530                                          is a dict containing reflections, as described in
531                                          the :ref:`Powder Reflections <PowderRefl_table>`
532                                          description.
533Instrument Parameters         \           A list containing two dicts where the possible
534                                          keys in each dict are listed below. The value
535                                          for each item is a list containing three values:
536                                          the initial value, the current value and a
537                                          refinement flag which can have a value of
538                                          True, False or 0 where 0 indicates a value that
539                                          cannot be refined. The first and second
540                                          values are floats unless otherwise noted.
541                                          Items in the first dict are noted as [1]
542\                         Lam             Specifies a wavelength in Angstroms [1]
543\                         Lam1            Specifies the primary wavelength in
544                                          Angstrom, when an alpha1, alpha2
545                                          source is used [1]
546\                         Lam2            Specifies the secondary wavelength in
547                                          Angstrom, when an alpha1, alpha2
548                                          source is used [1]
549                          I(L2)/I(L1)     Ratio of Lam2 to Lam1 [1]
550\                         Type            Histogram type (str) [1]:
551                                           * 'PXC' for constant wavelength x-ray
552                                           * 'PNC' for constant wavelength neutron
553                                           * 'PNT' for time of flight neutron
554\                         Zero            Two-theta zero correction in *degrees* [1]
555\                         Azimuth         Azimuthal setting angle for data recorded
556                                          with differing setting angles [1]
557\                         U, V, W         Cagliotti profile coefficients
558                                          for Gaussian instrumental broadening, where the
559                                          FWHM goes as
560                                          :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
561\                         X, Y            Cauchy (Lorentzian) instrumental broadening
562                                          coefficients [1]
563\                         SH/L            Variant of the Finger-Cox-Jephcoat asymmetric
564                                          peak broadening ratio. Note that this is the
565                                          average between S/L and H/L where S is
566                                          sample height, H is the slit height and
567                                          L is the goniometer diameter. [1]
568\                         Polariz.        Polarization coefficient. [1]
569wtFactor                      \           A weighting factor to increase or decrease
570                                          the leverage of data in the histogram (float).
571                                          A value of 1.0 weights the data with their
572                                          standard uncertainties and a larger value
573                                          increases the weighting of the data (equivalent
574                                          to decreasing the uncertainties).
575Sample Parameters             \           Specifies a dict with parameters that describe how
576                                          the data were collected, as listed
577                                          below. Refinable parameters are a list containing
578                                          a float and a bool, where the second value
579                                          specifies if the value is refined, otherwise
580                                          the value is a float unless otherwise noted.
581\                         Scale           The histogram scale factor (refinable)
582\                         Absorption      The sample absorption coefficient as
583                                          :math:`\\mu r` where r is the radius
584                                          (refinable). Only valid for Debye-Scherrer geometry.
585\                         SurfaceRoughA   Surface roughness parameter A as defined by
586                                          Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable -
587                                          only valid for Bragg-Brentano geometry)
588\                         SurfaceRoughB   Surface roughness parameter B (refinable -
589                                          only valid for Bragg-Brentano geometry)
590\                         DisplaceX,      Sample displacement from goniometer center
591                          DisplaceY       where Y is along the beam direction and
592                                          X is perpendicular. Units are :math:`\\mu m`
593                                          (refinable).
594\                         Phi, Chi,       Goniometer sample setting angles, in degrees.
595                          Omega
596\                         Gonio. radius   Radius of the diffractometer in mm
597\                         InstrName       A name for the instrument, used in preparing
598                                          a CIF (str).
599\                         Force,          Variables that describe how the measurement
600                          Temperature,    was performed. Not used directly in
601                          Humidity,       any computations.
602                          Pressure,
603                          Voltage
604\                         ranId           The random-number Id for the histogram
605                                          (same value as where top-level key is ranId)
606\                         Type            Type of diffraction data, may be 'Debye-Scherrer'
607                                          or 'Bragg-Brentano' (str).
608\                         Diffuse         not in use?
609hId                           \           The number assigned to the histogram when
610                                          the project is loaded or edited (can change)
611ranId                         \           A random number id for the histogram
612                                          that does not change
613Background                    \           The background is stored as a list with where
614                                          the first item in the list is list and the second
615                                          item is a dict. The list contains the background
616                                          function and its coefficients; the dict contains
617                                          Debye diffuse terms and background peaks.
618                                          (TODO: this needs to be expanded.)
619Data                          \           The data consist of a list of 6 np.arrays
620                                          containing in order:
621
622                                           0. the x-postions (two-theta in degrees),
623                                           1. the intensity values (Yobs),
624                                           2. the weights for each Yobs value
625                                           3. the computed intensity values (Ycalc)
626                                           4. the background values
627                                           5. Yobs-Ycalc
628======================  ===============  ====================================================
629
630Powder Reflection Data Structure
631--------------------------------
632
633.. _PowderRefl_table:
634
635.. index::
636   single: Powder reflection object description
637   single: Data object descriptions; Powder Reflections
638
639For every phase in a histogram, the ``Reflection Lists`` value is a dict
640one element of which is `'RefList'`, which is a np.array containing
641reflections. The columns in that array are documented below.
642
643==========  ====================================================
644  index         explanation
645==========  ====================================================
646 0,1,2       h,k,l (float)
647 3           multiplicity
648 4           d-space, Angstrom
649 5           pos, two-theta
650 6           sig, Gaussian width
651 7           gam, Lorenzian width
652 8           :math:`F_{obs}^2`
653 9           :math:`F_{calc}^2`
654 10          reflection phase, in degrees
655 11          intensity correction for reflection, this times
656             :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
657==========  ====================================================
658
659Single Crystal Tree Items
660-------------------------
661
662.. _Xtal_table:
663
664.. index::
665   single: Single Crystal data object description
666   single: Data object descriptions; Single crystal data
667
668Every single crystal diffraction histogram is stored in the GSAS-II data tree
669with a top-level entry named beginning with the string "HKLF ". The
670diffraction data for that information are directly associated with
671that tree item and there are a series of children to that item. The
672routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
673and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
674load this information into a dictionary where the child tree name is
675used as a key, and the information in the main entry is assigned
676a key of ``Data``, as outlined below.
677
678.. tabularcolumns:: |l|l|p{4in}|
679
680======================  ===============  ====================================================
681  key                      sub-key        explanation
682======================  ===============  ====================================================
683Data                          \           A dict that contains the
684                                          reflection table,
685                                          as described in the
686                                          :ref:`Single Crystal Reflections
687                                          <XtalRefl_table>`
688                                          description.
689
690Instrument Parameters         \           A list containing two dicts where the possible
691                                          keys in each dict are listed below. The value
692                                          for most items is a list containing two values:
693                                          the initial value, the current value.
694                                          The first and second
695                                          values are floats unless otherwise noted.
696\                         Lam             Specifies a wavelength in Angstroms (two floats)
697\                         Type            Histogram type (two str values):
698                                           * 'SXC' for constant wavelength x-ray
699                                           * 'SNC' for constant wavelength neutron
700                                           * 'SNT' for time of flight neutron
701\                         InstrName       A name for the instrument, used in preparing
702                                          a CIF (str).
703
704wtFactor                      \           A weighting factor to increase or decrease
705                                          the leverage of data in the histogram (float).
706                                          A value of 1.0 weights the data with their
707                                          standard uncertainties and a larger value
708                                          increases the weighting of the data (equivalent
709                                          to decreasing the uncertainties).
710
711hId                           \           The number assigned to the histogram when
712                                          the project is loaded or edited (can change)
713ranId                         \           A random number id for the histogram
714                                          that does not change
715======================  ===============  ====================================================
716
717Single Crystal Reflection Data Structure
718----------------------------------------
719
720.. _XtalRefl_table:
721
722.. index::
723   single: Single Crystal reflection object description
724   single: Data object descriptions; Single Crystal Reflections
725
726For every single crystal a histogram, the ``'Data'`` item contains
727the structure factors as an np.array in item `'RefList'`.
728The columns in that array are documented below.
729
730==========  ====================================================
731  index         explanation
732==========  ====================================================
733 0,1,2       h,k,l (float)
734 3           multiplicity
735 4           d-space, Angstrom
736 5           :math:`F_{obs}^2`
737 6           :math:`\sigma(F_{obs}^2)`
738 7           :math:`F_{calc}^2`
739 8           :math:`F_{obs}^2T`
740 9           :math:`F_{calc}^2T`
741 10          reflection phase, in degrees
742 11          intensity correction for reflection, this times
743             :math:`F_{obs}^2` or :math:`F_{calc}^2`
744             gives Iobs or Icalc
745==========  ====================================================
746
747Image Data Structure
748--------------------
749
750.. _Image_table:
751
752.. index::
753   image: Image data object description
754   image: Image object descriptions
755
756Every 2-dimensional image is stored in the GSAS-II data tree
757with a top-level entry named beginning with the string "IMG ". The
758image data are directly associated with that tree item and there
759are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
760and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
761load this information into a dictionary where the child tree name is
762used as a key, and the information in the main entry is assigned
763a key of ``Data``, as outlined below.
764
765.. tabularcolumns:: |l|l|p{4in}|
766
767======================  ======================  ====================================================
768  key                      sub-key              explanation
769======================  ======================  ====================================================
770Comments                       \                Text strings extracted from the original image data
771                                                header or a metafile. These cannot be changed by
772                                                the user; it may be empty.
773Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
774                                                value. Accomodates
775                                                detector orientations other than with the detector
776                                                X-axis
777                                                horizontal.
778\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
779                                                during image integration multiplied by value. It must have the same size/shape as
780                                                the integrated image. NB: value < 0 for subtraction.
781\                           calibrant           (str) The material used for determining the position/orientation
782                                                of the image. The data is obtained from :func:`ImageCalibrants`
783                                                and UserCalibrants.py (supplied by user).
784\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
785\                           calibskip           (int) The number of expected diffraction lines skipped during the last
786                                                calibration run.
787\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
788                                                strikes the detector plane as determined by calibration. This point
789                                                does not have to be within the limits of the detector boundaries.
790\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
791                                                of the image is at the center line otherwise it is at the leading edge.
792\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
793\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
794                                                calibration calculations. See pixLimit for details as how point is found.
795\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
796                                                ring offset at higher angles. Optionally determined by calibration.
797\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
798\                           distance            (float) The distance (mm) from sample to detector plane.
799\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
800                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
801                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
802                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
803                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
804\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
805\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
806\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
807                                                Required for texture calculations.
808\                           invert_x            (bool) If True display the image with the x-axis inverted.
809\                           invert_y            (bool) If True display the image with the y-axis inverted.
810\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
811\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
812\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
813                                                intensities obtained during integration.
814\                           outAzimuths         (int) The number of azimuth pie slices.
815\                           outChannels         (int) The number of 2-theta steps.
816\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
817\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
818                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
819                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
820                                                Locations are used to construct rings of points for calibration calcualtions.
821\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
822                                                integration using value.
823\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
824                                                diffraction ring with the same d-spacing (dsp)
825\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
826                                                selected by the user,
827\                           Range               (list) The minimum & maximum values of the image
828\                           rotation            (float) The angle between the x-axis and the vector about which the
829                                                detector is tilted. Constrained to -180 to 180 deg.
830\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
831                                                calculations.
832\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
833                                                to cause correction to be applied.
834\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
835\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
836\                           showLines           (bool) If True then isplay the integration limits to be used.
837\                           size                (list:int) The number of pixels on the image x & y axes
838\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
839\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
840\                           wavelength          (float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).
841
842Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
843                                                to be excluded from integration
844\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
845                                                of which is excluded from recalibration and integration. Only one frame is allowed.
846\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
847                                                from integration.
848\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
849                                                to be excluded from integration.
850\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
851                                                to be excluded from integration.
852\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
853                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
854
855Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
856\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
857                                                These will be restricted by space group symmetry; result of strain fit refinement.
858\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
859\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
860                                                and are used to determine the strain tensor.
861                                                The dictionary items are:
862                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
863                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
864                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
865                                                'Esig': (list: float) Esds for Emat from fitting.
866                                                'pixLimit': (int) Search range to find highest point on ring for each data point
867                                                'cutoff': (float) I/Ib cutoff for searching.
868                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
869                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
870                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
871
872======================  ======================  ====================================================
873
874Parameter Dictionary
875-------------------------
876
877.. _parmDict_table:
878
879.. index::
880   single: Parameter dictionary
881
882The parameter dictionary contains all of the variable parameters for the refinement.
883The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
884It is prepared in two ways. When loaded from the tree
885(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
886:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
887the values are lists with two elements: ``[value, refine flag]``
888
889When loaded from the GPX file (in
890:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
891dict is the actual parameter value (usually a float, but sometimes a
892letter or string flag value (such as I or A for iso/anisotropic).
893
894
895*Classes and routines*
896----------------------
897
898'''
899from __future__ import division, print_function
900import platform
901import re
902import imp
903import random as ran
904import sys
905import os.path as ospath
906if '2' in platform.python_version_tuple()[0]:
907    import cPickle
908else:
909    import pickle as cPickle
910import GSASIIpath
911import GSASIImath as G2mth
912import GSASIIspc as G2spc
913import numpy as np
914
915GSASIIpath.SetVersionNumber("$Revision: 3597 $")
916
917DefaultControls = {
918    'deriv type':'analytic Hessian',
919    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
920    'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
921    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
922    'Author':'no name',
923    'FreePrm1':'Sample humidity (%)',
924    'FreePrm2':'Sample voltage (V)',
925    'FreePrm3':'Applied load (MN)',
926    'ShowCell':False,
927    }
928'''Values to be used as defaults for the initial contents of the ``Controls``
929data tree item.
930'''
931def StripUnicode(string,subs='.'):
932    '''Strip non-ASCII characters from strings
933
934    :param str string: string to strip Unicode characters from
935    :param str subs: character(s) to place into string in place of each
936      Unicode character. Defaults to '.'
937
938    :returns: a new string with only ASCII characters
939    '''
940    s = ''
941    for c in string:
942        if ord(c) < 128:
943            s += c
944        else:
945            s += subs
946    return s
947#    return s.encode('ascii','replace')
948
949def MakeUniqueLabel(lbl,labellist):
950    '''Make sure that every a label is unique against a list by adding
951    digits at the end until it is not found in list.
952
953    :param str lbl: the input label
954    :param list labellist: the labels that have already been encountered
955    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
956      ``_10-99``, etc.) appended at the end
957    '''
958    lbl = StripUnicode(lbl.strip(),'_')
959    if not lbl: # deal with a blank label
960        lbl = '_1'
961    if lbl not in labellist:
962        labellist.append(lbl)
963        return lbl
964    i = 1
965    prefix = lbl
966    if '_' in lbl:
967        prefix = lbl[:lbl.rfind('_')]
968        suffix = lbl[lbl.rfind('_')+1:]
969        try:
970            i = int(suffix)+1
971        except: # suffix could not be parsed
972            i = 1
973            prefix = lbl
974    while prefix+'_'+str(i) in labellist:
975        i += 1
976    else:
977        lbl = prefix+'_'+str(i)
978        labellist.append(lbl)
979    return lbl
980
981PhaseIdLookup = {}
982'''dict listing phase name and random Id keyed by sequential phase index as a str;
983best to access this using :func:`LookupPhaseName`
984'''
985PhaseRanIdLookup = {}
986'''dict listing phase sequential index keyed by phase random Id;
987best to access this using :func:`LookupPhaseId`
988'''
989HistIdLookup = {}
990'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
991best to access this using :func:`LookupHistName`
992'''
993HistRanIdLookup = {}
994'''dict listing histogram sequential index keyed by histogram random Id;
995best to access this using :func:`LookupHistId`
996'''
997AtomIdLookup = {}
998'''dict listing for each phase index as a str, the atom label and atom random Id,
999keyed by atom sequential index as a str;
1000best to access this using :func:`LookupAtomLabel`
1001'''
1002AtomRanIdLookup = {}
1003'''dict listing for each phase the atom sequential index keyed by atom random Id;
1004best to access this using :func:`LookupAtomId`
1005'''
1006ShortPhaseNames = {}
1007'''a dict containing a possibly shortened and when non-unique numbered
1008version of the phase name. Keyed by the phase sequential index.
1009'''
1010ShortHistNames = {}
1011'''a dict containing a possibly shortened and when non-unique numbered
1012version of the histogram name. Keyed by the histogram sequential index.
1013'''
1014
1015VarDesc = {}
1016''' This dictionary lists descriptions for GSAS-II variables,
1017as set in :func:`CompileVarDesc`. See that function for a description
1018for how keys and values are written.
1019'''
1020
1021reVarDesc = {}
1022''' This dictionary lists descriptions for GSAS-II variables with
1023the same values as :attr:`VarDesc` except that keys have been compiled as
1024regular expressions. Initialized in :func:`CompileVarDesc`.
1025'''
1026# create a default space group object for P1; N.B. fails when building documentation
1027try:
1028    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1029except:
1030    pass
1031
1032def GetPhaseNames(fl):
1033    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1034    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1035
1036    :param file fl: opened .gpx file
1037    :return: list of phase names
1038    '''
1039    PhaseNames = []
1040    while True:
1041        try:
1042            data = cPickle.load(fl)
1043        except EOFError:
1044            break
1045        datum = data[0]
1046        if 'Phases' == datum[0]:
1047            for datus in data[1:]:
1048                PhaseNames.append(datus[0])
1049    fl.seek(0)          #reposition file
1050    return PhaseNames
1051
1052def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1053    '''Create a new phase dict with default values for various parameters
1054
1055    :param str Name: Name for new Phase
1056
1057    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1058      defaults to data for P 1
1059
1060    :param list cell: unit cell parameter list; defaults to
1061      [1.0,1.0,1.0,90.,90,90.,1.]
1062
1063    '''
1064    if SGData is None: SGData = P1SGData
1065    if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1066    phaseData = {
1067        'ranId':ran.randint(0,sys.maxsize),
1068        'General':{
1069            'Name':Name,
1070            'Type':'nuclear',
1071            'Modulated':False,
1072            'AtomPtrs':[3,1,7,9],
1073            'SGData':SGData,
1074            'Cell':[False,]+cell,
1075            'Pawley dmin':1.0,
1076            'Data plot type':'None',
1077            'SH Texture':{
1078                'Order':0,
1079                'Model':'cylindrical',
1080                'Sample omega':[False,0.0],
1081                'Sample chi':[False,0.0],
1082                'Sample phi':[False,0.0],
1083                'SH Coeff':[False,{}],
1084                'SHShow':False,
1085                'PFhkl':[0,0,1],
1086                'PFxyz':[0,0,1],
1087                'PlotType':'Pole figure',
1088                'Penalty':[['',],0.1,False,1.0]}},
1089        'Atoms':[],
1090        'Drawing':{},
1091        'Histograms':{},
1092        'Pawley ref':[],
1093        'RBModels':{},
1094        }
1095    if Super and Super.get('Use',False):
1096        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1097        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])[1]
1098        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1099
1100    return phaseData
1101
1102def ReadCIF(URLorFile):
1103    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1104    (from James Hester).
1105    The open routine gets confused with DOS names that begin with a letter and colon
1106    "C:\dir\" so this routine will try to open the passed name as a file and if that
1107    fails, try it as a URL
1108
1109    :param str URLorFile: string containing a URL or a file name. Code will try first
1110      to open it as a file and then as a URL.
1111
1112    :returns: a PyCifRW CIF object.
1113    '''
1114    import CifFile as cif # PyCifRW from James Hester
1115
1116    # alternate approach:
1117    #import urllib
1118    #ciffile = 'file:'+urllib.pathname2url(filename)
1119
1120    try:
1121        fp = open(URLorFile,'r')
1122        cf = cif.ReadCif(fp)
1123        fp.close()
1124        return cf
1125    except IOError:
1126        return cif.ReadCif(URLorFile)
1127
1128def IndexAllIds(Histograms,Phases):
1129    '''Scan through the used phases & histograms and create an index
1130    to the random numbers of phases, histograms and atoms. While doing this,
1131    confirm that assigned random numbers are unique -- just in case lightning
1132    strikes twice in the same place.
1133
1134    Note: this code assumes that the atom random Id (ranId) is the last
1135    element each atom record.
1136
1137    This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
1138    (which loads the histograms and phases from a GPX file),
1139    :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
1140    (which loads the histograms and phases from the data tree.) and
1141    :meth:`GSASIIconstrGUI.UpdateConstraints`
1142    (which displays & edits the constraints in a GUI)
1143
1144    TODO: do we need a lookup for rigid body variables?
1145    '''
1146    # process phases and atoms
1147    PhaseIdLookup.clear()
1148    PhaseRanIdLookup.clear()
1149    AtomIdLookup.clear()
1150    AtomRanIdLookup.clear()
1151    ShortPhaseNames.clear()
1152    for ph in Phases:
1153        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1154        ranId = Phases[ph]['ranId']
1155        while ranId in PhaseRanIdLookup:
1156            # Found duplicate random Id! note and reassign
1157            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1158            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1159        pId = str(Phases[ph]['pId'])
1160        PhaseIdLookup[pId] = (ph,ranId)
1161        PhaseRanIdLookup[ranId] = pId
1162        shortname = ph  #[:10]
1163        while shortname in ShortPhaseNames.values():
1164            shortname = ph[:8] + ' ('+ pId + ')'
1165        ShortPhaseNames[pId] = shortname
1166        AtomIdLookup[pId] = {}
1167        AtomRanIdLookup[pId] = {}
1168        for iatm,at in enumerate(Phases[ph]['Atoms']):
1169            ranId = at[cia+8]
1170            while ranId in AtomRanIdLookup[pId]: # check for dups
1171                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1172                at[cia+8] = ranId = ran.randint(0,sys.maxsize)
1173            AtomRanIdLookup[pId][ranId] = str(iatm)
1174            if Phases[ph]['General']['Type'] == 'macromolecular':
1175                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1176            else:
1177                label = at[ct-1]
1178            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1179    # process histograms
1180    HistIdLookup.clear()
1181    HistRanIdLookup.clear()
1182    ShortHistNames.clear()
1183    for hist in Histograms:
1184        ranId = Histograms[hist]['ranId']
1185        while ranId in HistRanIdLookup:
1186            # Found duplicate random Id! note and reassign
1187            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1188            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1189        hId = str(Histograms[hist]['hId'])
1190        HistIdLookup[hId] = (hist,ranId)
1191        HistRanIdLookup[ranId] = hId
1192        shortname = hist[:15]
1193        while shortname in ShortHistNames.values():
1194            shortname = hist[:11] + ' ('+ hId + ')'
1195        ShortHistNames[hId] = shortname
1196
1197def LookupAtomId(pId,ranId):
1198    '''Get the atom number from a phase and atom random Id
1199
1200    :param int/str pId: the sequential number of the phase
1201    :param int ranId: the random Id assigned to an atom
1202
1203    :returns: the index number of the atom (str)
1204    '''
1205    if not AtomRanIdLookup:
1206        raise Exception('Error: LookupAtomId called before IndexAllIds was run')
1207    if pId is None or pId == '':
1208        raise KeyError('Error: phase is invalid (None or blank)')
1209    pId = str(pId)
1210    if pId not in AtomRanIdLookup:
1211        raise KeyError('Error: LookupAtomId does not have phase '+pId)
1212    if ranId not in AtomRanIdLookup[pId]:
1213        raise KeyError('Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']')
1214    return AtomRanIdLookup[pId][ranId]
1215
1216def LookupAtomLabel(pId,index):
1217    '''Get the atom label from a phase and atom index number
1218
1219    :param int/str pId: the sequential number of the phase
1220    :param int index: the index of the atom in the list of atoms
1221
1222    :returns: the label for the atom (str) and the random Id of the atom (int)
1223    '''
1224    if not AtomIdLookup:
1225        raise Exception('Error: LookupAtomLabel called before IndexAllIds was run')
1226    if pId is None or pId == '':
1227        raise KeyError('Error: phase is invalid (None or blank)')
1228    pId = str(pId)
1229    if pId not in AtomIdLookup:
1230        raise KeyError('Error: LookupAtomLabel does not have phase '+pId)
1231    if index not in AtomIdLookup[pId]:
1232        raise KeyError('Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']')
1233    return AtomIdLookup[pId][index]
1234
1235def LookupPhaseId(ranId):
1236    '''Get the phase number and name from a phase random Id
1237
1238    :param int ranId: the random Id assigned to a phase
1239    :returns: the sequential Id (pId) number for the phase (str)
1240    '''
1241    if not PhaseRanIdLookup:
1242        raise Exception('Error: LookupPhaseId called before IndexAllIds was run')
1243    if ranId not in PhaseRanIdLookup:
1244        raise KeyError('Error: LookupPhaseId does not have ranId '+str(ranId))
1245    return PhaseRanIdLookup[ranId]
1246
1247def LookupPhaseName(pId):
1248    '''Get the phase number and name from a phase Id
1249
1250    :param int/str pId: the sequential assigned to a phase
1251    :returns:  (phase,ranId) where phase is the name of the phase (str)
1252      and ranId is the random # id for the phase (int)
1253    '''
1254    if not PhaseIdLookup:
1255        raise Exception('Error: LookupPhaseName called before IndexAllIds was run')
1256    if pId is None or pId == '':
1257        raise KeyError('Error: phase is invalid (None or blank)')
1258    pId = str(pId)
1259    if pId not in PhaseIdLookup:
1260        raise KeyError('Error: LookupPhaseName does not have index '+pId)
1261    return PhaseIdLookup[pId]
1262
1263def LookupHistId(ranId):
1264    '''Get the histogram number and name from a histogram random Id
1265
1266    :param int ranId: the random Id assigned to a histogram
1267    :returns: the sequential Id (hId) number for the histogram (str)
1268    '''
1269    if not HistRanIdLookup:
1270        raise Exception('Error: LookupHistId called before IndexAllIds was run')
1271    if ranId not in HistRanIdLookup:
1272        raise KeyError('Error: LookupHistId does not have ranId '+str(ranId))
1273    return HistRanIdLookup[ranId]
1274
1275def LookupHistName(hId):
1276    '''Get the histogram number and name from a histogram Id
1277
1278    :param int/str hId: the sequential assigned to a histogram
1279    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1280      and ranId is the random # id for the histogram (int)
1281    '''
1282    if not HistIdLookup:
1283        raise Exception('Error: LookupHistName called before IndexAllIds was run')
1284    if hId is None or hId == '':
1285        raise KeyError('Error: histogram is invalid (None or blank)')
1286    hId = str(hId)
1287    if hId not in HistIdLookup:
1288        raise KeyError('Error: LookupHistName does not have index '+hId)
1289    return HistIdLookup[hId]
1290
1291def fmtVarDescr(varname):
1292    '''Return a string with a more complete description for a GSAS-II variable
1293
1294    :param str varname: A full G2 variable name with 2 or 3 or 4
1295       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1296
1297    :returns: a string with the description
1298    '''
1299    s,l = VarDescr(varname)
1300    return s+": "+l
1301
1302def VarDescr(varname):
1303    '''Return two strings with a more complete description for a GSAS-II variable
1304
1305    :param str name: A full G2 variable name with 2 or 3 or 4
1306       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1307
1308    :returns: (loc,meaning) where loc describes what item the variable is mapped
1309      (phase, histogram, etc.) and meaning describes what the variable does.
1310    '''
1311
1312    # special handling for parameter names without a colons
1313    # for now, assume self-defining
1314    if varname.find(':') == -1:
1315        return "Global",varname
1316
1317    l = getVarDescr(varname)
1318    if not l:
1319        return ("invalid variable name ("+str(varname)+")!"),""
1320#        return "invalid variable name!",""
1321
1322    if not l[-1]:
1323        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1324
1325    if len(l) == 3:         #SASD variable name!
1326        s = 'component:'+l[1]
1327        return s,l[-1]
1328    s = ""
1329    if l[0] is not None and l[1] is not None: # HAP: keep short
1330        if l[2] == "Scale": # fix up ambigous name
1331            l[5] = "Phase fraction"
1332        if l[0] == '*':
1333            lbl = 'Seq. ref.'
1334        else:
1335            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1336        if l[1] == '*':
1337            hlbl = 'Seq. ref.'
1338        else:
1339            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1340        if hlbl[:4] == 'HKLF':
1341            hlbl = 'Xtl='+hlbl[5:]
1342        elif hlbl[:4] == 'PWDR':
1343            hlbl = 'Pwd='+hlbl[5:]
1344        else:
1345            hlbl = 'Hist='+hlbl
1346        s = "Ph="+str(lbl)+" * "+str(hlbl)
1347    else:
1348        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1349            l[5] = "Scale factor"
1350        if l[2] == 'Back': # background parameters are "special", alas
1351            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1352            l[-1] += ' #'+str(l[3])
1353        elif l[4] is not None: # rigid body parameter or modulation parm
1354            lbl = ShortPhaseNames.get(l[0],'phase?')
1355            if 'RB' in l[2]:    #rigid body parm
1356                s = "Res #"+str(l[3])+" body #"+str(l[4])+" in "+str(lbl)
1357            else: #modulation parm
1358                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1359        elif l[3] is not None: # atom parameter,
1360            lbl = ShortPhaseNames.get(l[0],'phase?')
1361            try:
1362                albl = LookupAtomLabel(l[0],l[3])[0]
1363            except KeyError:
1364                albl = 'Atom?'
1365            s = "Atom "+str(albl)+" in "+str(lbl)
1366        elif l[0] == '*':
1367            s = "All phases "
1368        elif l[0] is not None:
1369            lbl = ShortPhaseNames.get(l[0],'phase?')
1370            s = "Phase "+str(lbl)
1371        elif l[1] == '*':
1372            s = 'All hists'
1373        elif l[1] is not None:
1374            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1375            if hlbl[:4] == 'HKLF':
1376                hlbl = 'Xtl='+hlbl[5:]
1377            elif hlbl[:4] == 'PWDR':
1378                hlbl = 'Pwd='+hlbl[5:]
1379            else:
1380                hlbl = 'Hist='+hlbl
1381            s = str(hlbl)
1382    if not s:
1383        s = 'Global'
1384    return s,l[-1]
1385
1386def getVarDescr(varname):
1387    '''Return a short description for a GSAS-II variable
1388
1389    :param str name: A full G2 variable name with 2 or 3 or 4
1390       colons (<p>:<h>:name[:<a1>][:<a2>])
1391
1392    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1393      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1394      the histogram number and the atom number; `name` will always be
1395      a str; and `description` is str or `None`.
1396      If the variable name is incorrectly formed (for example, wrong
1397      number of colons), `None` is returned instead of a list.
1398    '''
1399    l = varname.split(':')
1400    if len(l) == 2:     #SASD parameter name
1401        return varname,l[0],getDescr(l[1])
1402    if len(l) == 3:
1403        l += [None,None]
1404    elif len(l) == 4:
1405        l += [None]
1406    elif len(l) != 5:
1407        return None
1408    for i in (0,1,3,4):
1409        if l[i] == "":
1410            l[i] = None
1411    l += [getDescr(l[2])]
1412    return l
1413
1414def CompileVarDesc():
1415    '''Set the values in the variable description lookup table (:attr:`VarDesc`)
1416    into :attr:`reVarDesc`. This is called in :func:`getDescr` so the initialization
1417    is always done before use.
1418
1419    Note that keys may contain regular expressions, where '[xyz]'
1420    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range of values).
1421    '.*' matches any string. For example::
1422
1423    'AUiso':'Atomic isotropic displacement parameter',
1424
1425    will match variable ``'p::AUiso:a'``.
1426    If parentheses are used in the key, the contents of those parentheses can be
1427    used in the value, such as::
1428
1429    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1430
1431    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1432    in the value when used.
1433
1434    '''
1435    if reVarDesc: return # already done
1436    for key,value in {
1437        # derived or other sequential vars
1438        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1439        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1440        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1441        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1442        # ambiguous, alas:
1443        'Scale' : 'Phase or Histogram scale factor',
1444        # Phase vars (p::<var>)
1445        'A([0-5])' : 'Reciprocal metric tensor component \\1',
1446        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1447        # Atom vars (p::<var>:a)
1448        'dA([xyz])$' : 'change to atomic coordinate, \\1',
1449        'A([xyz])$' : '\\1 fractional atomic coordinate',
1450        'AUiso':'Atomic isotropic displacement parameter',
1451        'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1452        'Afrac': 'Atomic site fraction parameter',
1453        'Amul': 'Atomic site multiplicity value',
1454        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1455        # Hist & Phase (HAP) vars (p:h:<var>)
1456        'Back': 'Background term',
1457        'BkPkint;(.*)':'Background peak #\\1 intensity',
1458        'BkPkpos;(.*)':'Background peak #\\1 position',
1459        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1460        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1461        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1462        'D([123][123])' : 'Anisotropic strain coef. \\1',
1463        'Extinction' : 'Extinction coef.',
1464        'MD' : 'March-Dollase coef.',
1465        'Mustrain;.*' : 'Microstrain coef.',
1466        'Size;.*' : 'Crystallite size value',
1467        'eA$' : 'Cubic mustrain value',
1468        'Ep$' : 'Primary extinction',
1469        'Es$' : 'Secondary type II extinction',
1470        'Eg$' : 'Secondary type I extinction',
1471        'Flack' : 'Flack parameter',
1472        'TwinFr' : 'Twin fraction',
1473        #Histogram vars (:h:<var>)
1474        'Absorption' : 'Absorption coef.',
1475        'Displace([XY])' : 'Debye-Scherrer sample displacement \\1',
1476        'Lam' : 'Wavelength',
1477        'I\(L2\)\/I\(L1\)' : 'Ka2/Ka1 intensity ratio',
1478        'Polariz\.' : 'Polarization correction',
1479        'SH/L' : 'FCJ peak asymmetry correction',
1480        '([UVW])$' : 'Gaussian instrument broadening \\1',
1481        '([XYZ])$' : 'Cauchy instrument broadening \\1',
1482        'Zero' : 'Debye-Scherrer zero correction',
1483        'Shift' : 'Bragg-Brentano sample displ.',
1484        'SurfRoughA' : 'Bragg-Brenano surface roughness A',
1485        'SurfRoughB' : 'Bragg-Brenano surface roughness B',
1486        'Transparency' : 'Bragg-Brentano sample tranparency',
1487        'DebyeA' : 'Debye model amplitude',
1488        'DebyeR' : 'Debye model radius',
1489        'DebyeU' : 'Debye model Uiso',
1490        'RBV.*' : 'Vector rigid body parameter',
1491        'RBR.*' : 'Residue rigid body parameter',
1492        'RBRO([aijk])' : 'Residue rigid body orientation parameter',
1493        'RBRP([xyz])' : 'Residue rigid body position parameter',
1494        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1495        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1496        'constr([0-9]*)' : 'Parameter from constraint',
1497        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1498        'mV([0-2])$' : 'Modulation vector component \\1',
1499        'Fsin'  :   'Sin site fraction modulation',
1500        'Fcos'  :   'Cos site fraction modulation',
1501        'Fzero'  :   'Crenel function offset',      #may go away
1502        'Fwid'   :   'Crenel function width',
1503        'Tmin'   :   'ZigZag/Block min location',
1504        'Tmax'   :   'ZigZag/Block max location',
1505        '([XYZ])max': 'ZigZag/Block max value for \\1',
1506        '([XYZ])sin'  : 'Sin position wave for \\1',
1507        '([XYZ])cos'  : 'Cos position wave for \\1',
1508        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1509        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1510        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1511        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1512        # PDF peak parms (l:<var>;l = peak no.)
1513        'PDFpos'  : 'PDF peak position',
1514        'PDFmag'  : 'PDF peak magnitude',
1515        'PDFsig'  : 'PDF peak std. dev.',
1516        # SASD vars (l:<var>;l = component)
1517        'Aspect ratio' : 'Particle aspect ratio',
1518        'Length' : 'Cylinder length',
1519        'Diameter' : 'Cylinder/disk diameter',
1520        'Thickness' : 'Disk thickness',
1521        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1522        'Dist' : 'Interparticle distance',
1523        'VolFr' : 'Dense scatterer volume fraction',
1524        'epis' : 'Sticky sphere epsilon',
1525        'Sticky' : 'Stickyness',
1526        'Depth' : 'Well depth',
1527        'Width' : 'Well width',
1528        'Volume' : 'Particle volume',
1529        'Radius' : 'Sphere/cylinder/disk radius',
1530        'Mean' : 'Particle mean radius',
1531        'StdDev' : 'Standard deviation in Mean',
1532        'G$': 'Guinier prefactor',
1533        'Rg$': 'Guinier radius of gyration',
1534        'B$': 'Porod prefactor',
1535        'P$': 'Porod power',
1536        'Cutoff': 'Porod cutoff',
1537        'PkInt': 'Bragg peak intensity',
1538        'PkPos': 'Bragg peak position',
1539        'PkSig': 'Bragg peak sigma',
1540        'PkGam': 'Bragg peak gamma',
1541        'e([12][12])' : 'strain tensor e\1',   # strain vars e11, e22, e12
1542        'Dcalc': 'Calc. d-spacing',
1543        'Back$': 'background parameter',
1544        'pos$': 'peak position',
1545        'int$': 'peak intensity',
1546        'WgtFrac':'phase weight fraction',
1547        'alpha':'TOF profile term',
1548        'beta-[01q]':'TOF profile term',
1549        'sig-[012q]':'TOF profile term',
1550        'dif[ABC]':'TOF to d-space calibration',
1551        'C\([0-9]*,[0-9]*\)' : 'spherical harmonics preferred orientation coef.',
1552        }.items():
1553        VarDesc[key] = value
1554        reVarDesc[re.compile(key)] = value
1555
1556def getDescr(name):
1557    '''Return a short description for a GSAS-II variable
1558
1559    :param str name: The descriptive part of the variable name without colons (:)
1560
1561    :returns: a short description or None if not found
1562    '''
1563
1564    CompileVarDesc() # compile the regular expressions, if needed
1565    for key in reVarDesc:
1566        m = key.match(name)
1567        if m:
1568            reVarDesc[key]
1569            return m.expand(reVarDesc[key])
1570    return None
1571
1572def GenWildCard(varlist):
1573    '''Generate wildcard versions of G2 variables. These introduce '*'
1574    for a phase, histogram or atom number (but only for one of these
1575    fields) but only when there is more than one matching variable in the
1576    input variable list. So if the input is this::
1577
1578      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
1579
1580    then the output will be this::
1581
1582       wildList = ['*::AUiso:0', '0::AUiso:*']
1583
1584    :param list varlist: an input list of GSAS-II variable names
1585      (such as 0::AUiso:0)
1586
1587    :returns: wildList, the generated list of wild card variable names.
1588    '''
1589    wild = []
1590    for i in (0,1,3):
1591        currentL = varlist[:]
1592        while currentL:
1593            item1 = currentL.pop(0)
1594            i1splt = item1.split(':')
1595            if i >= len(i1splt): continue
1596            if i1splt[i]:
1597                nextL = []
1598                i1splt[i] = '[0-9]+'
1599                rexp = re.compile(':'.join(i1splt))
1600                matchlist = [item1]
1601                for nxtitem in currentL:
1602                    if rexp.match(nxtitem):
1603                        matchlist += [nxtitem]
1604                    else:
1605                        nextL.append(nxtitem)
1606                if len(matchlist) > 1:
1607                    i1splt[i] = '*'
1608                    wild.append(':'.join(i1splt))
1609                currentL = nextL
1610    return wild
1611
1612def LookupWildCard(varname,varlist):
1613    '''returns a list of variable names from list varname
1614    that match wildcard name in varname
1615
1616    :param str varname: a G2 variable name containing a wildcard
1617      (such as \*::var)
1618    :param list varlist: the list of all variable names used in
1619      the current project
1620    :returns: a list of matching GSAS-II variables (may be empty)
1621    '''
1622    rexp = re.compile(varname.replace('*','[0-9]+'))
1623    return sorted([var for var in varlist if rexp.match(var)])
1624
1625
1626def _lookup(dic,key):
1627    '''Lookup a key in a dictionary, where None returns an empty string
1628    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
1629    '''
1630    if key is None:
1631        return ""
1632    elif key == "*":
1633        return "*"
1634    else:
1635        return dic.get(key,'?')
1636
1637def SortVariables(varlist):
1638    '''Sorts variable names in a sensible manner
1639    '''
1640    def cvnnums(var):
1641        v = []
1642        for i in var.split(':'):
1643            if i == '':
1644                v.append(-1)
1645                continue
1646            try:
1647                v.append(int(i))
1648            except:
1649                v.append(i)
1650        return v
1651    return sorted(varlist,key=cvnnums)
1652
1653class G2VarObj(object):
1654    '''Defines a GSAS-II variable either using the phase/atom/histogram
1655    unique Id numbers or using a character string that specifies
1656    variables by phase/atom/histogram number (which can change).
1657    Note that :func:`LoadID` should be used to (re)load the current Ids
1658    before creating or later using the G2VarObj object.
1659
1660    This can store rigid body variables, but does not translate the residue # and
1661    body # to/from random Ids
1662
1663    A :class:`G2VarObj` object can be created with a single parameter:
1664
1665    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
1666      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
1667
1668     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
1669     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
1670     * a is the atom number (which may be left blank in which case the third colon is omitted).
1671       The atom number can be specified as '*' if a phase number is specified (not as '*').
1672       For rigid body variables, specify a will be a string of form "residue:body#"
1673
1674      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
1675      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
1676      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
1677      For a rigid body variables, AtomID is a string of form "residue:body#".
1678
1679    If four positional arguments are supplied, they are:
1680
1681    :param str/int phasenum: The number for the phase (or None or '*')
1682    :param str/int histnum: The number for the histogram (or None or '*')
1683    :param str varname: a single value can be used to create a :class:`G2VarObj`
1684    :param str/int atomnum: The number for the atom (or None or '*')
1685
1686    '''
1687    IDdict = {}
1688    IDdict['phases'] = {}
1689    IDdict['hists'] = {}
1690    IDdict['atoms'] = {}
1691    def __init__(self,*args):
1692        self.phase = None
1693        self.histogram = None
1694        self.name = ''
1695        self.atom = None
1696        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
1697            # single arg with 4 values
1698            self.phase,self.histogram,self.name,self.atom = args[0]
1699        elif len(args) == 1 and ':' in args[0]:
1700            #parse a string
1701            lst = args[0].split(':')
1702            if lst[0] == '*':
1703                self.phase = '*'
1704                if len(lst) > 3:
1705                    self.atom = lst[3]
1706                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1707            elif lst[1] == '*':
1708                self.histogram = '*'
1709                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1710            else:
1711                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1712                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1713                if len(lst) == 4:
1714                    if lst[3] == '*':
1715                        self.atom = '*'
1716                    else:
1717                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
1718                elif len(lst) == 5:
1719                    self.atom = lst[3]+":"+lst[4]
1720                elif len(lst) == 3:
1721                    pass
1722                else:
1723                    raise Exception("Too many colons in var name "+str(args[0]))
1724            self.name = lst[2]
1725        elif len(args) == 4:
1726            if args[0] == '*':
1727                self.phase = '*'
1728                self.atom = args[3]
1729            else:
1730                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
1731                if args[3] == '*':
1732                    self.atom = '*'
1733                elif args[0] is not None:
1734                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
1735            if args[1] == '*':
1736                self.histogram = '*'
1737            else:
1738                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
1739            self.name = args[2]
1740        else:
1741            raise Exception("Incorrectly called GSAS-II parameter name")
1742
1743        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
1744
1745    def __str__(self):
1746        return self.varname()
1747
1748    def varname(self):
1749        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
1750        string (p:h:<var>:a) or (p:h:<var>)
1751
1752        :returns: the variable name as a str
1753        '''
1754        a = ""
1755        if self.phase == "*":
1756            ph = "*"
1757            if self.atom:
1758                a = ":" + str(self.atom)
1759        else:
1760            ph = _lookup(PhaseRanIdLookup,self.phase)
1761            if self.atom == '*':
1762                a = ':*'
1763            elif self.atom:
1764                if ":" in str(self.atom):
1765                    a = ":" + str(self.atom)
1766                elif ph in AtomRanIdLookup:
1767                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
1768                else:
1769                    a = ":?"
1770        if self.histogram == "*":
1771            hist = "*"
1772        else:
1773            hist = _lookup(HistRanIdLookup,self.histogram)
1774        s = (ph + ":" + hist + ":" + str(self.name)) + a
1775        return s
1776
1777    def __repr__(self):
1778        '''Return the detailed contents of the object
1779        '''
1780        s = "<"
1781        if self.phase == '*':
1782            s += "Phases: all; "
1783            if self.atom is not None:
1784                if ":" in str(self.atom):
1785                    s += "Rigid body" + str(self.atom) + "; "
1786                else:
1787                    s += "Atom #" + str(self.atom) + "; "
1788        elif self.phase is not None:
1789            ph =  _lookup(PhaseRanIdLookup,self.phase)
1790            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
1791            if self.atom == '*':
1792                s += "Atoms: all; "
1793            elif ":" in str(self.atom):
1794                s += "Rigid body" + str(self.atom) + "; "
1795            elif self.atom is not None:
1796                s += "Atom rId=" + str(self.atom)
1797                if ph in AtomRanIdLookup:
1798                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
1799                else:
1800                    s += " (#? -- not found!); "
1801        if self.histogram == '*':
1802            s += "Histograms: all; "
1803        elif self.histogram is not None:
1804            hist = _lookup(HistRanIdLookup,self.histogram)
1805            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
1806        s += 'Variable name="' + str(self.name) + '">'
1807        return s+" ("+self.varname()+")"
1808
1809    def __eq__(self, other):
1810        if type(other) is type(self):
1811            return (self.phase == other.phase and
1812                    self.histogram == other.histogram and
1813                    self.name == other.name and
1814                    self.atom == other.atom)
1815        return False
1816
1817    def _show(self):
1818        'For testing, shows the current lookup table'
1819        print ('phases'+ self.IDdict['phases'])
1820        print ('hists'+ self.IDdict['hists'])
1821        print ('atomDict'+ self.IDdict['atoms'])
1822
1823#==========================================================================
1824def SetDefaultSample():
1825    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
1826    return {
1827        'InstrName':'',
1828        'ranId':ran.randint(0,sys.maxsize),
1829        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
1830        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],'Diffuse':[],
1831        'Temperature':300.,'Pressure':0.1,'Time':0.0,
1832        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
1833        'Gonio. radius':200.0,
1834        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
1835#SASD items
1836        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
1837        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
1838        'Trans':1.0,                            #measured transmission
1839        'SlitLen':0.0,                          #Slit length - in Q(A-1)
1840        }
1841######################################################################
1842class ImportBaseclass(object):
1843    '''Defines a base class for the reading of input files (diffraction
1844    data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1845    for an explanation on how to use a subclass of this class.
1846    '''
1847    class ImportException(Exception):
1848        '''Defines an Exception that is used when an import routine hits an expected error,
1849        usually in .Reader.
1850
1851        Good practice is that the Reader should define a value in self.errors that
1852        tells the user some information about what is wrong with their file.
1853        '''
1854        pass
1855
1856    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
1857    def __init__(self,formatName,longFormatName=None,
1858                 extensionlist=[],strictExtension=False,):
1859        self.formatName = formatName # short string naming file type
1860        if longFormatName: # longer string naming file type
1861            self.longFormatName = longFormatName
1862        else:
1863            self.longFormatName = formatName
1864        # define extensions that are allowed for the file type
1865        # for windows, remove any extensions that are duplicate, as case is ignored
1866        if sys.platform == 'windows' and extensionlist:
1867            extensionlist = list(set([s.lower() for s in extensionlist]))
1868        self.extensionlist = extensionlist
1869        # If strictExtension is True, the file will not be read, unless
1870        # the extension matches one in the extensionlist
1871        self.strictExtension = strictExtension
1872        self.errors = ''
1873        self.warnings = ''
1874        self.SciPy = False          #image reader needed scipy
1875        # used for readers that will use multiple passes to read
1876        # more than one data block
1877        self.repeat = False
1878        self.selections = []
1879        self.repeatcount = 0
1880        self.readfilename = '?'
1881        self.scriptable = False
1882        #print 'created',self.__class__
1883
1884    def ReInitialize(self):
1885        'Reinitialize the Reader to initial settings'
1886        self.errors = ''
1887        self.warnings = ''
1888        self.SciPy = False          #image reader needed scipy
1889        self.repeat = False
1890        self.repeatcount = 0
1891        self.readfilename = '?'
1892
1893
1894#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1895#        '''This method must be supplied in the child class to read the file.
1896#        if the read fails either return False or raise an Exception
1897#        preferably of type ImportException.
1898#        '''
1899#        #start reading
1900#        raise ImportException("Error occurred while...")
1901#        self.errors += "Hint for user on why the error occur
1902#        return False # if an error occurs
1903#        return True # if read OK
1904
1905    def ExtensionValidator(self, filename):
1906        '''This methods checks if the file has the correct extension
1907       
1908        :returns:
1909       
1910          * False if this filename will not be supported by this reader (only
1911            when strictExtension is True)
1912          * True if the extension matches the list supplied by the reader
1913          * None if the reader allows un-registered extensions
1914         
1915        '''
1916        if filename:
1917            ext = ospath.splitext(filename)[1]
1918            if not ext and self.strictExtension: return False
1919            for ext in self.extensionlist:               
1920                if sys.platform == 'windows':
1921                    if filename.lower().endswith(ext): return True
1922                else:
1923                    if filename.endswith(ext): return True
1924        if self.strictExtension:
1925            return False
1926        else:
1927            return None
1928
1929    def ContentsValidator(self, filename):
1930        '''This routine will attempt to determine if the file can be read
1931        with the current format.
1932        This will typically be overridden with a method that
1933        takes a quick scan of [some of]
1934        the file contents to do a "sanity" check if the file
1935        appears to match the selected format.
1936        the file must be opened here with the correct format (binary/text)
1937        '''
1938        #filepointer.seek(0) # rewind the file pointer
1939        return True
1940
1941    def CIFValidator(self, filepointer):
1942        '''A :meth:`ContentsValidator` for use to validate CIF files.
1943        '''
1944        filepointer.seek(0)
1945        for i,l in enumerate(filepointer):
1946            if i >= 1000: return True
1947            '''Encountered only blank lines or comments in first 1000
1948            lines. This is unlikely, but assume it is CIF anyway, since we are
1949            even less likely to find a file with nothing but hashes and
1950            blank lines'''
1951            line = l.strip()
1952            if len(line) == 0: # ignore blank lines
1953                continue
1954            elif line.startswith('#'): # ignore comments
1955                continue
1956            elif line.startswith('data_'): # on the right track, accept this file
1957                return True
1958            else: # found something invalid
1959                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1960                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1961                    self.errors += '  '+str(l)
1962                else:
1963                    self.errors += '  (binary)'
1964                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
1965                self.errors += '\n        a data_ statement begins a block.'
1966                return False
1967
1968######################################################################
1969class ImportPhase(ImportBaseclass):
1970    '''Defines a base class for the reading of files with coordinates
1971
1972    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1973    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase`.
1974    See :ref:`Writing a Import Routine<Import_Routines>`
1975    for an explanation on how to use this class.
1976
1977    '''
1978    def __init__(self,formatName,longFormatName=None,extensionlist=[],
1979        strictExtension=False,):
1980        # call parent __init__
1981        ImportBaseclass.__init__(self,formatName,longFormatName,
1982            extensionlist,strictExtension)
1983        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1984        self.Constraints = None
1985
1986######################################################################
1987class ImportStructFactor(ImportBaseclass):
1988    '''Defines a base class for the reading of files with tables
1989    of structure factors.
1990
1991    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
1992    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
1993    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1994    :meth:`Reader`.
1995
1996    See :ref:`Writing a Import Routine<Import_Routines>`
1997    for an explanation on how to use import classes in general. The specifics
1998    for reading a structure factor histogram require that
1999    the ``Reader()`` routine in the import
2000    class need to do only a few things: It
2001    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2002    and set :attr:`Parameters` with the instrument parameters
2003    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2004    '''
2005    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2006        strictExtension=False,):
2007        ImportBaseclass.__init__(self,formatName,longFormatName,
2008            extensionlist,strictExtension)
2009
2010        # define contents of Structure Factor entry
2011        self.Parameters = []
2012        'self.Parameters is a list with two dicts for data parameter settings'
2013        self.InitParameters()
2014        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2015        self.Banks = []             #for multi bank data (usually TOF)
2016        '''self.RefDict is a dict containing the reflection information, as read from the file.
2017        Item 'RefList' contains the reflection information. See the
2018        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
2019        for the contents of each row. Dict element 'FF'
2020        contains the form factor values for each element type; if this entry
2021        is left as initialized (an empty list) it will be initialized as needed later.
2022        '''
2023    def ReInitialize(self):
2024        'Reinitialize the Reader to initial settings'
2025        ImportBaseclass.ReInitialize(self)
2026        self.InitParameters()
2027        self.Banks = []             #for multi bank data (usually TOF)
2028        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2029
2030    def InitParameters(self):
2031        'initialize the instrument parameters structure'
2032        Lambda = 0.70926
2033        HistType = 'SXC'
2034        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2035                            'Lam':[Lambda,Lambda]
2036                            }, {}]
2037        'Parameters is a list with two dicts for data parameter settings'
2038
2039    def UpdateParameters(self,Type=None,Wave=None):
2040        'Revise the instrument parameters'
2041        if Type is not None:
2042            self.Parameters[0]['Type'] = [Type,Type]
2043        if Wave is not None:
2044            self.Parameters[0]['Lam'] = [Wave,Wave]
2045
2046######################################################################
2047class ImportPowderData(ImportBaseclass):
2048    '''Defines a base class for the reading of files with powder data.
2049
2050    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2051    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder`.
2052    See :ref:`Writing a Import Routine<Import_Routines>`
2053    for an explanation on how to use this class.
2054    '''
2055    def __init__(self,formatName,longFormatName=None,
2056        extensionlist=[],strictExtension=False,):
2057        ImportBaseclass.__init__(self,formatName,longFormatName,
2058            extensionlist,strictExtension)
2059        self.clockWd = None  # used in TOF
2060        self.ReInitialize()
2061
2062    def ReInitialize(self):
2063        'Reinitialize the Reader to initial settings'
2064        ImportBaseclass.ReInitialize(self)
2065        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2066        self.powderdata = [] # Powder dataset
2067        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2068                np.array(x), # x-axis values
2069                np.array(y), # powder pattern intensities
2070                np.array(w), # 1/sig(intensity)^2 values (weights)
2071                np.array(yc), # calc. intensities (zero)
2072                np.array(yb), # calc. background (zero)
2073                np.array(yd), # obs-calc profiles
2074        '''
2075        self.comments = []
2076        self.idstring = ''
2077        self.Sample = SetDefaultSample() # default sample parameters
2078        self.Controls = {}  # items to be placed in top-level Controls
2079        self.GSAS = None     # used in TOF
2080        self.repeat_instparm = True # Should a parm file be
2081        #                             used for multiple histograms?
2082        self.instparm = None # name hint from file of instparm to use
2083        self.instfile = '' # full path name to instrument parameter file
2084        self.instbank = '' # inst parm bank number
2085        self.instmsg = ''  # a label that gets printed to show
2086                           # where instrument parameters are from
2087        self.numbanks = 1
2088        self.instdict = {} # place items here that will be transferred to the instrument parameters
2089        self.pwdparms = {} # place parameters that are transferred directly to the tree
2090                           # here (typically from an existing GPX file)
2091######################################################################
2092class ImportSmallAngleData(ImportBaseclass):
2093    '''Defines a base class for the reading of files with small angle data.
2094    See :ref:`Writing a Import Routine<Import_Routines>`
2095    for an explanation on how to use this class.
2096    '''
2097    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2098        strictExtension=False,):
2099
2100        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2101            strictExtension)
2102        self.ReInitialize()
2103
2104    def ReInitialize(self):
2105        'Reinitialize the Reader to initial settings'
2106        ImportBaseclass.ReInitialize(self)
2107        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2108        self.smallangledata = [] # SASD dataset
2109        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2110                np.array(x), # x-axis values
2111                np.array(y), # powder pattern intensities
2112                np.array(w), # 1/sig(intensity)^2 values (weights)
2113                np.array(yc), # calc. intensities (zero)
2114                np.array(yd), # obs-calc profiles
2115                np.array(yb), # preset bkg
2116        '''
2117        self.comments = []
2118        self.idstring = ''
2119        self.Sample = SetDefaultSample()
2120        self.GSAS = None     # used in TOF
2121        self.clockWd = None  # used in TOF
2122        self.numbanks = 1
2123        self.instdict = {} # place items here that will be transferred to the instrument parameters
2124
2125######################################################################
2126class ImportReflectometryData(ImportBaseclass):
2127    '''Defines a base class for the reading of files with reflectometry data.
2128    See :ref:`Writing a Import Routine<Import_Routines>`
2129    for an explanation on how to use this class.
2130    '''
2131    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2132        strictExtension=False,):
2133
2134        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2135            strictExtension)
2136        self.ReInitialize()
2137
2138    def ReInitialize(self):
2139        'Reinitialize the Reader to initial settings'
2140        ImportBaseclass.ReInitialize(self)
2141        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2142        self.reflectometrydata = [] # SASD dataset
2143        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2144                np.array(x), # x-axis values
2145                np.array(y), # powder pattern intensities
2146                np.array(w), # 1/sig(intensity)^2 values (weights)
2147                np.array(yc), # calc. intensities (zero)
2148                np.array(yd), # obs-calc profiles
2149                np.array(yb), # preset bkg
2150        '''
2151        self.comments = []
2152        self.idstring = ''
2153        self.Sample = SetDefaultSample()
2154        self.GSAS = None     # used in TOF
2155        self.clockWd = None  # used in TOF
2156        self.numbanks = 1
2157        self.instdict = {} # place items here that will be transferred to the instrument parameters
2158
2159######################################################################
2160class ImportPDFData(ImportBaseclass):
2161    '''Defines a base class for the reading of files with PDF G(R) data.
2162    See :ref:`Writing a Import Routine<Import_Routines>`
2163    for an explanation on how to use this class.
2164    '''
2165    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2166        strictExtension=False,):
2167
2168        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2169            strictExtension)
2170        self.ReInitialize()
2171
2172    def ReInitialize(self):
2173        'Reinitialize the Reader to initial settings'
2174        ImportBaseclass.ReInitialize(self)
2175        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2176        self.pdfdata = [] # PDF G(R) dataset
2177        '''A pdf g(r) data set is a list with items [x,y]:
2178                np.array(x), # r-axis values
2179                np.array(y), # pdf g(r)
2180        '''
2181        self.comments = []
2182        self.idstring = ''
2183        self.numbanks = 1
2184
2185######################################################################
2186class ImportImage(ImportBaseclass):
2187    '''Defines a base class for the reading of images
2188
2189    Images are read in only these places:
2190
2191      * Initial reading is typically done from a menu item
2192        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2193        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2194        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2195        :meth:`Reader`. This returns a list of reader objects for each read image.
2196
2197      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2198        directly into the data tree.
2199
2200      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2201
2202    .. _Image_import_routines:
2203
2204    When reading an image, the ``Reader()`` routine in the ImportImage class
2205    should set:
2206
2207      * :attr:`Comments`: a list of strings (str),
2208      * :attr:`Npix`: the number of pixels in the image (int),
2209      * :attr:`Image`: the actual image as a numpy array (np.array)
2210      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2211        data items are needed:
2212
2213         * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2214         * 'wavelength': wavelength in Angstoms.
2215         * 'distance': distance of detector from sample in cm.
2216         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2217         * 'size': size of image (such as ``[2048,2048]``).
2218         * 'ImageTag': image number or other keyword used to retrieve image from
2219           a multi-image data file (defaults to ``1`` if not specified).
2220         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2221
2222    optional data items:
2223
2224      * :attr:`repeat`: set to True if there are additional images to
2225        read in the file, False otherwise
2226      * :attr:`repeatcount`: set to the number of the image.
2227
2228    Note that the above is initialized with :meth:`InitParameters`.
2229    (Also see :ref:`Writing a Import Routine<Import_Routines>`
2230    for an explanation on how to use import classes in general.)
2231    '''
2232    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2233        strictExtension=False,):
2234        ImportBaseclass.__init__(self,formatName,longFormatName,
2235            extensionlist,strictExtension)
2236        self.InitParameters()
2237
2238    def ReInitialize(self):
2239        'Reinitialize the Reader to initial settings -- not used at present'
2240        ImportBaseclass.ReInitialize(self)
2241        self.InitParameters()
2242
2243    def InitParameters(self):
2244        'initialize the instrument parameters structure'
2245        self.Comments = ['No comments']
2246        self.Data = {}
2247        self.Npix = 0
2248        self.Image = None
2249        self.repeat = False
2250        self.repeatcount = 1
2251        self.sumfile = ''
2252
2253    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2254        '''Optionally, call this after reading in an image to load it into the tree.
2255        This saves time by preventing a reread of the same information.
2256        '''
2257        if ParentFrame:
2258            ParentFrame.ImageZ = self.Image   # store the image for plotting
2259            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2260            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2261
2262#################################################################################################
2263# shortcut routines
2264exp = np.exp
2265sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2266cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2267tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2268sqrt = sq = lambda x: np.sqrt(x)
2269pi = lambda: np.pi
2270class ExpressionObj(object):
2271    '''Defines an object with a user-defined expression, to be used for
2272    secondary fits or restraints. Object is created null, but is changed
2273    using :meth:`LoadExpression`. This contains only the minimum
2274    information that needs to be stored to save and load the expression
2275    and how it is mapped to GSAS-II variables.
2276    '''
2277    def __init__(self):
2278        self.expression = ''
2279        'The expression as a text string'
2280        self.assgnVars = {}
2281        '''A dict where keys are label names in the expression mapping to a GSAS-II
2282        variable. The value a G2 variable name.
2283        Note that the G2 variable name may contain a wild-card and correspond to
2284        multiple values.
2285        '''
2286        self.freeVars = {}
2287        '''A dict where keys are label names in the expression mapping to a free
2288        parameter. The value is a list with:
2289
2290         * a name assigned to the parameter
2291         * a value for to the parameter and
2292         * a flag to determine if the variable is refined.
2293        '''
2294        self.depVar = None
2295
2296        self.lastError = ('','')
2297        '''Shows last encountered error in processing expression
2298        (list of 1-3 str values)'''
2299
2300        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2301        self.distance_atoms = None  # to be used for defining atom distances
2302
2303    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2304        '''Load the expression and associated settings into the object. Raises
2305        an exception if the expression is not parsed, if not all functions
2306        are defined or if not all needed parameter labels in the expression
2307        are defined.
2308
2309        This will not test if the variable referenced in these definitions
2310        are actually in the parameter dictionary. This is checked when the
2311        computation for the expression is done in :meth:`SetupCalc`.
2312
2313        :param str expr: the expression
2314        :param list exprVarLst: parameter labels found in the expression
2315        :param dict varSelect: this will be 0 for Free parameters
2316          and non-zero for expression labels linked to G2 variables.
2317        :param dict varName: Defines a name (str) associated with each free parameter
2318        :param dict varValue: Defines a value (float) associated with each free parameter
2319        :param dict varRefflag: Defines a refinement flag (bool)
2320          associated with each free parameter
2321        '''
2322        self.expression = expr
2323        self.compiledExpr = None
2324        self.freeVars = {}
2325        self.assgnVars = {}
2326        for v in exprVarLst:
2327            if varSelect[v] == 0:
2328                self.freeVars[v] = [
2329                    varName.get(v),
2330                    varValue.get(v),
2331                    varRefflag.get(v),
2332                    ]
2333            else:
2334                self.assgnVars[v] = varName[v]
2335        self.CheckVars()
2336
2337    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2338        '''Load the expression and associated settings from the object into
2339        arrays used for editing.
2340
2341        :param list exprVarLst: parameter labels found in the expression
2342        :param dict varSelect: this will be 0 for Free parameters
2343          and non-zero for expression labels linked to G2 variables.
2344        :param dict varName: Defines a name (str) associated with each free parameter
2345        :param dict varValue: Defines a value (float) associated with each free parameter
2346        :param dict varRefflag: Defines a refinement flag (bool)
2347          associated with each free parameter
2348
2349        :returns: the expression as a str
2350        '''
2351        for v in self.freeVars:
2352            varSelect[v] = 0
2353            varName[v] = self.freeVars[v][0]
2354            varValue[v] = self.freeVars[v][1]
2355            varRefflag[v] = self.freeVars[v][2]
2356        for v in self.assgnVars:
2357            varSelect[v] = 1
2358            varName[v] = self.assgnVars[v]
2359        return self.expression
2360
2361    def GetVaried(self):
2362        'Returns the names of the free parameters that will be refined'
2363        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
2364
2365    def GetVariedVarVal(self):
2366        'Returns the names and values of the free parameters that will be refined'
2367        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
2368
2369    def UpdateVariedVars(self,varyList,values):
2370        'Updates values for the free parameters (after a refinement); only updates refined vars'
2371        for v in self.freeVars:
2372            if not self.freeVars[v][2]: continue
2373            if "::"+self.freeVars[v][0] not in varyList: continue
2374            indx = list(varyList).index("::"+self.freeVars[v][0])
2375            self.freeVars[v][1] = values[indx]
2376
2377    def GetIndependentVars(self):
2378        'Returns the names of the required independent parameters used in expression'
2379        return [self.assgnVars[v] for v in self.assgnVars]
2380
2381    def CheckVars(self):
2382        '''Check that the expression can be parsed, all functions are
2383        defined and that input loaded into the object is internally
2384        consistent. If not an Exception is raised.
2385
2386        :returns: a dict with references to packages needed to
2387          find functions referenced in the expression.
2388        '''
2389        ret = self.ParseExpression(self.expression)
2390        if not ret:
2391            raise Exception("Expression parse error")
2392        exprLblList,fxnpkgdict = ret
2393        # check each var used in expression is defined
2394        defined = list(self.assgnVars.keys()) + list(self.freeVars.keys())
2395        notfound = []
2396        for var in exprLblList:
2397            if var not in defined:
2398                notfound.append(var)
2399        if notfound:
2400            msg = 'Not all variables defined'
2401            msg1 = 'The following variables were not defined: '
2402            msg2 = ''
2403            for var in notfound:
2404                if msg: msg += ', '
2405                msg += var
2406            self.lastError = (msg1,'  '+msg2)
2407            raise Exception(msg)
2408        return fxnpkgdict
2409
2410    def ParseExpression(self,expr):
2411        '''Parse an expression and return a dict of called functions and
2412        the variables used in the expression. Returns None in case an error
2413        is encountered. If packages are referenced in functions, they are loaded
2414        and the functions are looked up into the modules global
2415        workspace.
2416
2417        Note that no changes are made to the object other than
2418        saving an error message, so that this can be used for testing prior
2419        to the save.
2420
2421        :returns: a list of used variables
2422        '''
2423        self.lastError = ('','')
2424        import ast
2425        def FindFunction(f):
2426            '''Find the object corresponding to function f
2427            :param str f: a function name such as 'numpy.exp'
2428            :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2429              that defines the package location(s) and where pkgobj
2430              defines the object associated with the function.
2431              If the function is not found, pkgobj is None.
2432            '''
2433            df = f.split('.')
2434            pkgdict = {}
2435            # no listed package, try in current namespace
2436            if len(df) == 1:
2437                try:
2438                    fxnobj = eval(f)
2439                    return pkgdict,fxnobj
2440                except (AttributeError, NameError):
2441                    return None,None
2442            else:
2443                try:
2444                    fxnobj = eval(f)
2445                    pkgdict[df[0]] = eval(df[0])
2446                    return pkgdict,fxnobj
2447                except (AttributeError, NameError):
2448                    pass
2449            # includes a package, lets try to load the packages
2450            pkgname = ''
2451            path = sys.path+['./',]
2452            for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2453                if pkgname:
2454                    pkgname += '.' + pkg
2455                else:
2456                    pkgname = pkg
2457                fp = None
2458                try:
2459                    fp, fppath,desc = imp.find_module(pkg,path)
2460                    pkgobj = imp.load_module(pkg,fp,fppath,desc)
2461                    pkgdict[pkgname] = pkgobj
2462                    path = [fppath]
2463                except Exception as msg:
2464                    print('load of '+pkgname+' failed with error='+str(msg))
2465                    return {},None
2466                finally:
2467                    if fp: fp.close()
2468                try:
2469                    #print 'before',pkgdict.keys()
2470                    fxnobj = eval(f,globals(),pkgdict)
2471                    #print 'after 1',pkgdict.keys()
2472                    #fxnobj = eval(f,pkgdict)
2473                    #print 'after 2',pkgdict.keys()
2474                    return pkgdict,fxnobj
2475                except:
2476                    continue
2477            return None # not found
2478        def ASTtransverse(node,fxn=False):
2479            '''Transverse a AST-parsed expresson, compiling a list of variables
2480            referenced in the expression. This routine is used recursively.
2481
2482            :returns: varlist,fxnlist where
2483              varlist is a list of referenced variable names and
2484              fxnlist is a list of used functions
2485            '''
2486            varlist = []
2487            fxnlist = []
2488            if isinstance(node, list):
2489                for b in node:
2490                    v,f = ASTtransverse(b,fxn)
2491                    varlist += v
2492                    fxnlist += f
2493            elif isinstance(node, ast.AST):
2494                for a, b in ast.iter_fields(node):
2495                    if isinstance(b, ast.AST):
2496                        if a == 'func':
2497                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
2498                            continue
2499                        v,f = ASTtransverse(b,fxn)
2500                        varlist += v
2501                        fxnlist += f
2502                    elif isinstance(b, list):
2503                        v,f = ASTtransverse(b,fxn)
2504                        varlist += v
2505                        fxnlist += f
2506                    elif node.__class__.__name__ == "Name":
2507                        varlist += [b]
2508                    elif fxn and node.__class__.__name__ == "Attribute":
2509                        varlist += [b]
2510            return varlist,fxnlist
2511        try:
2512            exprast = ast.parse(expr)
2513        except SyntaxError:
2514            s = ''
2515            import traceback
2516            for i in traceback.format_exc().splitlines()[-3:-1]:
2517                if s: s += "\n"
2518                s += str(i)
2519            self.lastError = ("Error parsing expression:",s)
2520            return
2521        # find the variables & functions
2522        v,f = ASTtransverse(exprast)
2523        varlist = sorted(list(set(v)))
2524        fxnlist = list(set(f))
2525        pkgdict = {}
2526        # check the functions are defined
2527        for fxn in fxnlist:
2528            fxndict,fxnobj = FindFunction(fxn)
2529            if not fxnobj:
2530                self.lastError = ("Error: Invalid function",fxn,
2531                                  "is not defined")
2532                return
2533            if not hasattr(fxnobj,'__call__'):
2534                self.lastError = ("Error: Not a function.",fxn,
2535                                  "cannot be called as a function")
2536                return
2537            pkgdict.update(fxndict)
2538        return varlist,pkgdict
2539
2540    def GetDepVar(self):
2541        'return the dependent variable, or None'
2542        return self.depVar
2543
2544    def SetDepVar(self,var):
2545        'Set the dependent variable, if used'
2546        self.depVar = var
2547#==========================================================================
2548class ExpressionCalcObj(object):
2549    '''An object used to evaluate an expression from a :class:`ExpressionObj`
2550    object.
2551
2552    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
2553      an expression string and mappings for the parameter labels in that object.
2554    '''
2555    def __init__(self,exprObj):
2556        self.eObj = exprObj
2557        'The expression and mappings; a :class:`ExpressionObj` object'
2558        self.compiledExpr = None
2559        'The expression as compiled byte-code'
2560        self.exprDict = {}
2561        '''dict that defines values for labels used in expression and packages
2562        referenced by functions
2563        '''
2564        self.lblLookup = {}
2565        '''Lookup table that specifies the expression label name that is
2566        tied to a particular GSAS-II parameters in the parmDict.
2567        '''
2568        self.fxnpkgdict = {}
2569        '''a dict with references to packages needed to
2570        find functions referenced in the expression.
2571        '''
2572        self.varLookup = {}
2573        '''Lookup table that specifies the GSAS-II variable(s)
2574        indexed by the expression label name. (Used for only for diagnostics
2575        not evaluation of expression.)
2576        '''
2577        self.su = None
2578        '''Standard error evaluation where supplied by the evaluator
2579        '''
2580        # Patch: for old-style expressions with a (now removed step size)
2581        if '2' in platform.python_version_tuple()[0]: 
2582            basestr = basestring
2583        else:
2584            basestr = str
2585        for v in self.eObj.assgnVars:
2586            if not isinstance(self.eObj.assgnVars[v], basestr):
2587                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
2588        self.parmDict = {}
2589        '''A copy of the parameter dictionary, for distance and angle computation
2590        '''
2591
2592    def SetupCalc(self,parmDict):
2593        '''Do all preparations to use the expression for computation.
2594        Adds the free parameter values to the parameter dict (parmDict).
2595        '''
2596        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2597            return
2598        self.fxnpkgdict = self.eObj.CheckVars()
2599        # all is OK, compile the expression
2600        self.compiledExpr = compile(self.eObj.expression,'','eval')
2601
2602        # look at first value in parmDict to determine its type
2603        parmsInList = True
2604        if '2' in platform.python_version_tuple()[0]: 
2605            basestr = basestring
2606        else:
2607            basestr = str
2608        for key in parmDict:
2609            val = parmDict[key]
2610            if isinstance(val, basestr):
2611                parmsInList = False
2612                break
2613            try: # check if values are in lists
2614                val = parmDict[key][0]
2615            except (TypeError,IndexError):
2616                parmsInList = False
2617            break
2618
2619        # set up the dicts needed to speed computations
2620        self.exprDict = {}
2621        self.lblLookup = {}
2622        self.varLookup = {}
2623        for v in self.eObj.freeVars:
2624            varname = self.eObj.freeVars[v][0]
2625            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
2626            self.lblLookup[varname] = v
2627            self.varLookup[v] = varname
2628            if parmsInList:
2629                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
2630            else:
2631                parmDict[varname] = self.eObj.freeVars[v][1]
2632            self.exprDict[v] = self.eObj.freeVars[v][1]
2633        for v in self.eObj.assgnVars:
2634            varname = self.eObj.assgnVars[v]
2635            if varname in parmDict:
2636                self.lblLookup[varname] = v
2637                self.varLookup[v] = varname
2638                if parmsInList:
2639                    self.exprDict[v] = parmDict[varname][0]
2640                else:
2641                    self.exprDict[v] = parmDict[varname]
2642            elif '*' in varname:
2643                varlist = LookupWildCard(varname,list(parmDict.keys()))
2644                if len(varlist) == 0:
2645                    raise Exception("No variables match "+str(v))
2646                for var in varlist:
2647                    self.lblLookup[var] = v
2648                if parmsInList:
2649                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
2650                else:
2651                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
2652                self.varLookup[v] = [var for var in varlist]
2653            else:
2654                self.exprDict[v] = None
2655#                raise Exception,"No value for variable "+str(v)
2656        self.exprDict.update(self.fxnpkgdict)
2657
2658    def UpdateVars(self,varList,valList):
2659        '''Update the dict for the expression with a set of values
2660        :param list varList: a list of variable names
2661        :param list valList: a list of corresponding values
2662        '''
2663        for var,val in zip(varList,valList):
2664            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
2665
2666    def UpdateDict(self,parmDict):
2667        '''Update the dict for the expression with values in a dict
2668        :param list parmDict: a dict of values some of which may be in use here
2669        '''
2670        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2671            self.parmDict = parmDict
2672            return
2673        for var in parmDict:
2674            if var in self.lblLookup:
2675                self.exprDict[self.lblLookup[var]] = parmDict[var]
2676
2677    def EvalExpression(self):
2678        '''Evaluate an expression. Note that the expression
2679        and mapping are taken from the :class:`ExpressionObj` expression object
2680        and the parameter values were specified in :meth:`SetupCalc`.
2681        :returns: a single value for the expression. If parameter
2682        values are arrays (for example, from wild-carded variable names),
2683        the sum of the resulting expression is returned.
2684
2685        For example, if the expression is ``'A*B'``,
2686        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
2687
2688        [0.5, 1, 0.5]
2689
2690        then the result will be ``4.0``.
2691        '''
2692        self.su = None
2693        if self.eObj.expression.startswith('Dist'):
2694#            GSASIIpath.IPyBreak()
2695            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
2696            return dist
2697        elif self.eObj.expression.startswith('Angle'):
2698            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
2699            return angle
2700        if self.compiledExpr is None:
2701            raise Exception("EvalExpression called before SetupCalc")
2702        try:
2703            val = eval(self.compiledExpr,globals(),self.exprDict)
2704        except TypeError:
2705            val = None
2706        if not np.isscalar(val):
2707            val = np.sum(val)
2708        return val
2709
2710class G2Exception(Exception):
2711    def __init__(self,msg):
2712        self.msg = msg
2713    def __str__(self):
2714        return repr(self.msg)
2715
2716def HowDidIgetHere(wherecalledonly=False):
2717    '''Show a traceback with calls that brought us to the current location.
2718    Used for debugging.
2719    '''
2720    import traceback
2721    if wherecalledonly:
2722        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
2723        print(i.strip().rstrip())
2724    else:
2725        print (70*'*')
2726        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
2727        print (70*'*')
2728
2729def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
2730    '''Create and initialize a new set of PDF tree entries
2731
2732    :param Frame G2frame: main GSAS-II tree frame object
2733    :param str PWDRtree: name of PWDR to be used to create PDF item
2734    :param dict ElList: data structure with composition
2735    :param list Qlimits: Q limits to be used for computing the PDF
2736    :param float numAtm: no. atom in chemical formula
2737    :param float FltBkg: flat background value
2738    :param list PDFnames: previously used PDF names
2739
2740    :returns: the Id of the newly created PDF entry
2741    '''
2742    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
2743    if PDFname in PDFnames:
2744        print('Skipping, entry already exists: '+PDFname)
2745        return None
2746    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
2747    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
2748    Data = {
2749        'Sample':{'Name':PWDRtree,'Mult':1.0},
2750        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
2751        'Container':{'Name':'','Mult':-1.0,'Refine':False},
2752        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
2753        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
2754        'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
2755        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,'Rmin':1.0,
2756        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
2757    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
2758    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
2759        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
2760    return Id
2761
2762class ShowTiming(object):
2763    '''An object to use for timing repeated sections of code.
2764
2765    Create the object with::
2766       tim0 = ShowTiming()
2767
2768    Tag sections of code to be timed with::
2769       tim0.start('start')
2770       tim0.start('in section 1')
2771       tim0.start('in section 2')
2772       
2773    etc. (Note that each section should have a unique label.)
2774
2775    After the last section, end timing with::
2776       tim0.end()
2777
2778    Show timing results with::
2779       tim0.show()
2780       
2781    '''
2782    import time
2783    def __init__(self):
2784        self.timeSum =  []
2785        self.timeStart = []
2786        self.label = []
2787        self.prev = None
2788    def start(self,label):
2789        if label in self.label:
2790            i = self.label.index(label)
2791            self.timeStart[i] = time.time()
2792        else:
2793            i = len(self.label)
2794            self.timeSum.append(0.0)
2795            self.timeStart.append(time.time())
2796            self.label.append(label)
2797        if self.prev is not None:
2798            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
2799        self.prev = i
2800    def end(self):
2801        if self.prev is not None:
2802            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
2803        self.prev = None
2804    def show(self):
2805        sumT = sum(self.timeSum)
2806        print('Timing results (total={:.2f} sec)'.format(sumT))
2807        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
2808            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
2809
2810
2811if __name__ == "__main__":
2812    # test equation evaluation
2813    def showEQ(calcobj):
2814        print (50*'=')
2815        print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
2816        for v in sorted(calcobj.varLookup):
2817            print ("  "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
2818        # print '  Derivatives'
2819        # for v in calcobj.derivStep.keys():
2820        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
2821
2822    obj = ExpressionObj()
2823
2824    obj.expression = "A*np.exp(B)"
2825    obj.assgnVars =  {'B': '0::Afrac:1'}
2826    obj.freeVars =  {'A': [u'A', 0.5, True]}
2827    #obj.CheckVars()
2828    calcobj = ExpressionCalcObj(obj)
2829
2830    obj1 = ExpressionObj()
2831    obj1.expression = "A*np.exp(B)"
2832    obj1.assgnVars =  {'B': '0::Afrac:*'}
2833    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
2834    #obj.CheckVars()
2835    calcobj1 = ExpressionCalcObj(obj1)
2836
2837    obj2 = ExpressionObj()
2838    obj2.distance_stuff = np.array([[0,1],[1,-1]])
2839    obj2.expression = "Dist(1,2)"
2840    GSASIIpath.InvokeDebugOpts()
2841    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
2842    calcobj2 = ExpressionCalcObj(obj2)
2843    calcobj2.SetupCalc(parmDict2)
2844    showEQ(calcobj2)
2845
2846    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
2847    print ('\nDict = '+parmDict1)
2848    calcobj.SetupCalc(parmDict1)
2849    showEQ(calcobj)
2850    calcobj1.SetupCalc(parmDict1)
2851    showEQ(calcobj1)
2852
2853    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
2854    print ('Dict = '+parmDict2)
2855    calcobj.SetupCalc(parmDict2)
2856    showEQ(calcobj)
2857    calcobj1.SetupCalc(parmDict2)
2858    showEQ(calcobj1)
2859    calcobj2.SetupCalc(parmDict2)
2860    showEQ(calcobj2)
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