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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2017-11-06 22:32:17 +0000 (Mon, 06 Nov 2017) $
5# $Author: vondreele $
6# $Revision: 3151 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 3151 2017-11-06 22:32:17Z 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: 3151 $")
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 TypeError:
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'])
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        'Polariz\.' : 'Polarization correction',
1478        'SH/L' : 'FCJ peak asymmetry correction',
1479        '([UVW])$' : 'Gaussian instrument broadening \\1',
1480        '([XY])$' : 'Cauchy instrument broadening \\1',
1481        'Zero' : 'Debye-Scherrer zero correction',
1482        'nDebye' : 'Debye model background corr. terms',
1483        'nPeaks' : 'Fixed peak background corr. terms',
1484        'RBV.*' : 'Vector rigid body parameter',
1485        'RBR.*' : 'Residue rigid body parameter',
1486        'RBRO([aijk])' : 'Residue rigid body orientation parameter',
1487        'RBRP([xyz])' : 'Residue rigid body position parameter',
1488        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1489        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1490        'constr([0-9]*)' : 'Parameter from constraint',
1491        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1492        'mV([0-2])$' : 'Modulation vector component \\1',
1493        'Fsin'  :   'Sin site fraction modulation',
1494        'Fcos'  :   'Cos site fraction modulation',
1495        'Fzero'  :   'Crenel function offset',      #may go away
1496        'Fwid'   :   'Crenel function width',
1497        'Tmin'   :   'ZigZag/Block min location',
1498        'Tmax'   :   'ZigZag/Block max location',
1499        '([XYZ])max': 'ZigZag/Block max value for \\1',
1500        '([XYZ])sin'  : 'Sin position wave for \\1',
1501        '([XYZ])cos'  : 'Cos position wave for \\1',
1502        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1503        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1504        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1505        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1506        # PDF peak parms (l:<var>;l = peak no.)
1507        'PDFpos'  : 'PDF peak position',
1508        'PDFmag'  : 'PDF peak magnitude',
1509        'PDFsig'  : 'PDF peak std. dev.',
1510        # SASD vars (l:<var>;l = component)
1511        'Aspect ratio' : 'Particle aspect ratio',
1512        'Length' : 'Cylinder length',
1513        'Diameter' : 'Cylinder/disk diameter',
1514        'Thickness' : 'Disk thickness',
1515        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1516        'Dist' : 'Interparticle distance',
1517        'VolFr' : 'Dense scatterer volume fraction',
1518        'epis' : 'Sticky sphere epsilon',
1519        'Sticky' : 'Stickyness',
1520        'Depth' : 'Well depth',
1521        'Width' : 'Well width',
1522        'Volume' : 'Particle volume',
1523        'Radius' : 'Sphere/cylinder/disk radius',
1524        'Mean' : 'Particle mean radius',
1525        'StdDev' : 'Standard deviation in Mean',
1526        'G$': 'Guinier prefactor',
1527        'Rg$': 'Guinier radius of gyration',
1528        'B$': 'Porod prefactor',
1529        'P$': 'Porod power',
1530        'Cutoff': 'Porod cutoff',
1531        'PkInt': 'Bragg peak intensity',
1532        'PkPos': 'Bragg peak position',
1533        'PkSig': 'Bragg peak sigma',
1534        'PkGam': 'Bragg peak gamma',
1535        'e([12][12])' : 'strain tensor e\1',   # strain vars e11, e22, e12
1536        'Dcalc': 'Calc. d-spacing',
1537        'Back$': 'background parameter',
1538        'pos$': 'peak position',
1539        'int$': 'peak intensity',
1540        'WgtFrac':'phase weight fraction',
1541        'C\([0-9]*,[0-9]*\)' : 'spherical harmonics preferred orientation coef.',
1542        }.items():
1543        VarDesc[key] = value
1544        reVarDesc[re.compile(key)] = value
1545
1546def getDescr(name):
1547    '''Return a short description for a GSAS-II variable
1548
1549    :param str name: The descriptive part of the variable name without colons (:)
1550
1551    :returns: a short description or None if not found
1552    '''
1553
1554    CompileVarDesc() # compile the regular expressions, if needed
1555    for key in reVarDesc:
1556        m = key.match(name)
1557        if m:
1558            reVarDesc[key]
1559            return m.expand(reVarDesc[key])
1560    return None
1561
1562def GenWildCard(varlist):
1563    '''Generate wildcard versions of G2 variables. These introduce '*'
1564    for a phase, histogram or atom number (but only for one of these
1565    fields) but only when there is more than one matching variable in the
1566    input variable list. So if the input is this::
1567
1568      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
1569
1570    then the output will be this::
1571
1572       wildList = ['*::AUiso:0', '0::AUiso:*']
1573
1574    :param list varlist: an input list of GSAS-II variable names
1575      (such as 0::AUiso:0)
1576
1577    :returns: wildList, the generated list of wild card variable names.
1578    '''
1579    wild = []
1580    for i in (0,1,3):
1581        currentL = varlist[:]
1582        while currentL:
1583            item1 = currentL.pop(0)
1584            i1splt = item1.split(':')
1585            if i >= len(i1splt): continue
1586            if i1splt[i]:
1587                nextL = []
1588                i1splt[i] = '[0-9]+'
1589                rexp = re.compile(':'.join(i1splt))
1590                matchlist = [item1]
1591                for nxtitem in currentL:
1592                    if rexp.match(nxtitem):
1593                        matchlist += [nxtitem]
1594                    else:
1595                        nextL.append(nxtitem)
1596                if len(matchlist) > 1:
1597                    i1splt[i] = '*'
1598                    wild.append(':'.join(i1splt))
1599                currentL = nextL
1600    return wild
1601
1602def LookupWildCard(varname,varlist):
1603    '''returns a list of variable names from list varname
1604    that match wildcard name in varname
1605
1606    :param str varname: a G2 variable name containing a wildcard
1607      (such as \*::var)
1608    :param list varlist: the list of all variable names used in
1609      the current project
1610    :returns: a list of matching GSAS-II variables (may be empty)
1611    '''
1612    rexp = re.compile(varname.replace('*','[0-9]+'))
1613    return sorted([var for var in varlist if rexp.match(var)])
1614
1615
1616def _lookup(dic,key):
1617    '''Lookup a key in a dictionary, where None returns an empty string
1618    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
1619    '''
1620    if key is None:
1621        return ""
1622    elif key == "*":
1623        return "*"
1624    else:
1625        return dic.get(key,'?')
1626
1627def SortVariables(varlist):
1628    '''Sorts variable names in a sensible manner
1629    '''
1630    def cvnnums(var):
1631        v = []
1632        for i in var.split(':'):
1633            try:
1634                v.append(int(i))
1635            except:
1636                v.append(i)
1637        return v
1638    return sorted(varlist,key=cvnnums)
1639
1640class G2VarObj(object):
1641    '''Defines a GSAS-II variable either using the phase/atom/histogram
1642    unique Id numbers or using a character string that specifies
1643    variables by phase/atom/histogram number (which can change).
1644    Note that :func:`LoadID` should be used to (re)load the current Ids
1645    before creating or later using the G2VarObj object.
1646
1647    This can store rigid body variables, but does not translate the residue # and
1648    body # to/from random Ids
1649
1650    A :class:`G2VarObj` object can be created with a single parameter:
1651
1652    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
1653      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
1654
1655     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
1656     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
1657     * a is the atom number (which may be left blank in which case the third colon is omitted).
1658       The atom number can be specified as '*' if a phase number is specified (not as '*').
1659       For rigid body variables, specify a will be a string of form "residue:body#"
1660
1661      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
1662      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
1663      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
1664      For a rigid body variables, AtomID is a string of form "residue:body#".
1665
1666    If four positional arguments are supplied, they are:
1667
1668    :param str/int phasenum: The number for the phase (or None or '*')
1669    :param str/int histnum: The number for the histogram (or None or '*')
1670    :param str varname: a single value can be used to create a :class:`G2VarObj`
1671    :param str/int atomnum: The number for the atom (or None or '*')
1672
1673    '''
1674    IDdict = {}
1675    IDdict['phases'] = {}
1676    IDdict['hists'] = {}
1677    IDdict['atoms'] = {}
1678    def __init__(self,*args):
1679        self.phase = None
1680        self.histogram = None
1681        self.name = ''
1682        self.atom = None
1683        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
1684            # single arg with 4 values
1685            self.phase,self.histogram,self.name,self.atom = args[0]
1686        elif len(args) == 1 and ':' in args[0]:
1687            #parse a string
1688            lst = args[0].split(':')
1689            if lst[0] == '*':
1690                self.phase = '*'
1691                if len(lst) > 3:
1692                    self.atom = lst[3]
1693                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1694            elif lst[1] == '*':
1695                self.histogram = '*'
1696                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1697            else:
1698                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1699                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1700                if len(lst) == 4:
1701                    if lst[3] == '*':
1702                        self.atom = '*'
1703                    else:
1704                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
1705                elif len(lst) == 5:
1706                    self.atom = lst[3]+":"+lst[4]
1707                elif len(lst) == 3:
1708                    pass
1709                else:
1710                    raise Exception("Too many colons in var name "+str(args[0]))
1711            self.name = lst[2]
1712        elif len(args) == 4:
1713            if args[0] == '*':
1714                self.phase = '*'
1715                self.atom = args[3]
1716            else:
1717                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
1718                if args[3] == '*':
1719                    self.atom = '*'
1720                elif args[0] is not None:
1721                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
1722            if args[1] == '*':
1723                self.histogram = '*'
1724            else:
1725                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
1726            self.name = args[2]
1727        else:
1728            raise Exception("Incorrectly called GSAS-II parameter name")
1729
1730        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
1731
1732    def __str__(self):
1733        return self.varname()
1734
1735    def varname(self):
1736        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
1737        string (p:h:<var>:a) or (p:h:<var>)
1738
1739        :returns: the variable name as a str
1740        '''
1741        a = ""
1742        if self.phase == "*":
1743            ph = "*"
1744            if self.atom:
1745                a = ":" + str(self.atom)
1746        else:
1747            ph = _lookup(PhaseRanIdLookup,self.phase)
1748            if self.atom == '*':
1749                a = ':*'
1750            elif self.atom:
1751                if ":" in str(self.atom):
1752                    a = ":" + str(self.atom)
1753                elif ph in AtomRanIdLookup:
1754                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
1755                else:
1756                    a = ":?"
1757        if self.histogram == "*":
1758            hist = "*"
1759        else:
1760            hist = _lookup(HistRanIdLookup,self.histogram)
1761        s = (ph + ":" + hist + ":" + str(self.name)) + a
1762        return s
1763
1764    def __repr__(self):
1765        '''Return the detailed contents of the object
1766        '''
1767        s = "<"
1768        if self.phase == '*':
1769            s += "Phases: all; "
1770            if self.atom is not None:
1771                if ":" in str(self.atom):
1772                    s += "Rigid body" + str(self.atom) + "; "
1773                else:
1774                    s += "Atom #" + str(self.atom) + "; "
1775        elif self.phase is not None:
1776            ph =  _lookup(PhaseRanIdLookup,self.phase)
1777            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
1778            if self.atom == '*':
1779                s += "Atoms: all; "
1780            elif ":" in str(self.atom):
1781                s += "Rigid body" + str(self.atom) + "; "
1782            elif self.atom is not None:
1783                s += "Atom rId=" + str(self.atom)
1784                if ph in AtomRanIdLookup:
1785                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
1786                else:
1787                    s += " (#? -- not found!); "
1788        if self.histogram == '*':
1789            s += "Histograms: all; "
1790        elif self.histogram is not None:
1791            hist = _lookup(HistRanIdLookup,self.histogram)
1792            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
1793        s += 'Variable name="' + str(self.name) + '">'
1794        return s+" ("+self.varname()+")"
1795
1796    def __eq__(self, other):
1797        if type(other) is type(self):
1798            return (self.phase == other.phase and
1799                    self.histogram == other.histogram and
1800                    self.name == other.name and
1801                    self.atom == other.atom)
1802        return False
1803
1804    def _show(self):
1805        'For testing, shows the current lookup table'
1806        print ('phases'+ self.IDdict['phases'])
1807        print ('hists'+ self.IDdict['hists'])
1808        print ('atomDict'+ self.IDdict['atoms'])
1809
1810#==========================================================================
1811def SetDefaultSample():
1812    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
1813    return {
1814        'InstrName':'',
1815        'ranId':ran.randint(0,sys.maxsize),
1816        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
1817        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],'Diffuse':[],
1818        'Temperature':300.,'Pressure':0.1,'Time':0.0,
1819        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
1820        'Gonio. radius':200.0,
1821        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
1822#SASD items
1823        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
1824        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
1825        'Trans':1.0,                            #measured transmission
1826        'SlitLen':0.0,                          #Slit length - in Q(A-1)
1827        }
1828######################################################################
1829class ImportBaseclass(object):
1830    '''Defines a base class for the reading of input files (diffraction
1831    data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1832    for an explanation on how to use a subclass of this class.
1833    '''
1834    class ImportException(Exception):
1835        '''Defines an Exception that is used when an import routine hits an expected error,
1836        usually in .Reader.
1837
1838        Good practice is that the Reader should define a value in self.errors that
1839        tells the user some information about what is wrong with their file.
1840        '''
1841        pass
1842
1843    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
1844    def __init__(self,formatName,longFormatName=None,
1845                 extensionlist=[],strictExtension=False,):
1846        self.formatName = formatName # short string naming file type
1847        if longFormatName: # longer string naming file type
1848            self.longFormatName = longFormatName
1849        else:
1850            self.longFormatName = formatName
1851        # define extensions that are allowed for the file type
1852        # for windows, remove any extensions that are duplicate, as case is ignored
1853        if sys.platform == 'windows' and extensionlist:
1854            extensionlist = list(set([s.lower() for s in extensionlist]))
1855        self.extensionlist = extensionlist
1856        # If strictExtension is True, the file will not be read, unless
1857        # the extension matches one in the extensionlist
1858        self.strictExtension = strictExtension
1859        self.errors = ''
1860        self.warnings = ''
1861        self.SciPy = False          #image reader needed scipy
1862        # used for readers that will use multiple passes to read
1863        # more than one data block
1864        self.repeat = False
1865        self.selections = []
1866        self.repeatcount = 0
1867        self.readfilename = '?'
1868        self.scriptable = False
1869        #print 'created',self.__class__
1870
1871    def ReInitialize(self):
1872        'Reinitialize the Reader to initial settings'
1873        self.errors = ''
1874        self.warnings = ''
1875        self.SciPy = False          #image reader needed scipy
1876        self.repeat = False
1877        self.repeatcount = 0
1878        self.readfilename = '?'
1879
1880
1881#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1882#        '''This method must be supplied in the child class to read the file.
1883#        if the read fails either return False or raise an Exception
1884#        preferably of type ImportException.
1885#        '''
1886#        #start reading
1887#        raise ImportException("Error occurred while...")
1888#        self.errors += "Hint for user on why the error occur
1889#        return False # if an error occurs
1890#        return True # if read OK
1891
1892    def ExtensionValidator(self, filename):
1893        '''This methods checks if the file has the correct extension
1894        Return False if this filename will not be supported by this reader
1895        Return True if the extension matches the list supplied by the reader
1896        Return None if the reader allows un-registered extensions
1897        '''
1898        if filename:
1899            ext = ospath.splitext(filename)[1]
1900            if sys.platform == 'windows': ext = ext.lower()
1901            if ext in self.extensionlist: return True
1902            if self.strictExtension: return False
1903        return 
1904
1905    def ContentsValidator(self, filename):
1906        '''This routine will attempt to determine if the file can be read
1907        with the current format.
1908        This will typically be overridden with a method that
1909        takes a quick scan of [some of]
1910        the file contents to do a "sanity" check if the file
1911        appears to match the selected format.
1912        the file must be opened here with the correct format (binary/text)
1913        '''
1914        #filepointer.seek(0) # rewind the file pointer
1915        return True
1916
1917    def CIFValidator(self, filepointer):
1918        '''A :meth:`ContentsValidator` for use to validate CIF files.
1919        '''
1920        filepointer.seek(0)
1921        for i,l in enumerate(filepointer):
1922            if i >= 1000: return True
1923            '''Encountered only blank lines or comments in first 1000
1924            lines. This is unlikely, but assume it is CIF anyway, since we are
1925            even less likely to find a file with nothing but hashes and
1926            blank lines'''
1927            line = l.strip()
1928            if len(line) == 0: # ignore blank lines
1929                continue
1930            elif line.startswith('#'): # ignore comments
1931                continue
1932            elif line.startswith('data_'): # on the right track, accept this file
1933                return True
1934            else: # found something invalid
1935                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1936                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1937                    self.errors += '  '+str(l)
1938                else:
1939                    self.errors += '  (binary)'
1940                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
1941                self.errors += '\n        a data_ statement begins a block.'
1942                return False
1943
1944######################################################################
1945class ImportPhase(ImportBaseclass):
1946    '''Defines a base class for the reading of files with coordinates
1947
1948    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1949    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase`.
1950    See :ref:`Writing a Import Routine<Import_Routines>`
1951    for an explanation on how to use this class.
1952
1953    '''
1954    def __init__(self,formatName,longFormatName=None,extensionlist=[],
1955        strictExtension=False,):
1956        # call parent __init__
1957        ImportBaseclass.__init__(self,formatName,longFormatName,
1958            extensionlist,strictExtension)
1959        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1960        self.Constraints = None
1961
1962######################################################################
1963class ImportStructFactor(ImportBaseclass):
1964    '''Defines a base class for the reading of files with tables
1965    of structure factors.
1966
1967    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
1968    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
1969    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1970    :meth:`Reader`.
1971
1972    See :ref:`Writing a Import Routine<Import_Routines>`
1973    for an explanation on how to use import classes in general. The specifics
1974    for reading a structure factor histogram require that
1975    the ``Reader()`` routine in the import
1976    class need to do only a few things: It
1977    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1978    and set :attr:`Parameters` with the instrument parameters
1979    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1980    '''
1981    def __init__(self,formatName,longFormatName=None,extensionlist=[],
1982        strictExtension=False,):
1983        ImportBaseclass.__init__(self,formatName,longFormatName,
1984            extensionlist,strictExtension)
1985
1986        # define contents of Structure Factor entry
1987        self.Parameters = []
1988        'self.Parameters is a list with two dicts for data parameter settings'
1989        self.InitParameters()
1990        self.RefDict = {'RefList':[],'FF':{},'Super':0}
1991        self.Banks = []             #for multi bank data (usually TOF)
1992        '''self.RefDict is a dict containing the reflection information, as read from the file.
1993        Item 'RefList' contains the reflection information. See the
1994        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1995        for the contents of each row. Dict element 'FF'
1996        contains the form factor values for each element type; if this entry
1997        is left as initialized (an empty list) it will be initialized as needed later.
1998        '''
1999    def ReInitialize(self):
2000        'Reinitialize the Reader to initial settings'
2001        ImportBaseclass.ReInitialize(self)
2002        self.InitParameters()
2003        self.Banks = []             #for multi bank data (usually TOF)
2004        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2005
2006    def InitParameters(self):
2007        'initialize the instrument parameters structure'
2008        Lambda = 0.70926
2009        HistType = 'SXC'
2010        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2011                            'Lam':[Lambda,Lambda]
2012                            }, {}]
2013        'Parameters is a list with two dicts for data parameter settings'
2014
2015    def UpdateParameters(self,Type=None,Wave=None):
2016        'Revise the instrument parameters'
2017        if Type is not None:
2018            self.Parameters[0]['Type'] = [Type,Type]
2019        if Wave is not None:
2020            self.Parameters[0]['Lam'] = [Wave,Wave]
2021
2022######################################################################
2023class ImportPowderData(ImportBaseclass):
2024    '''Defines a base class for the reading of files with powder data.
2025
2026    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2027    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder`.
2028    See :ref:`Writing a Import Routine<Import_Routines>`
2029    for an explanation on how to use this class.
2030    '''
2031    def __init__(self,formatName,longFormatName=None,
2032        extensionlist=[],strictExtension=False,):
2033        ImportBaseclass.__init__(self,formatName,longFormatName,
2034            extensionlist,strictExtension)
2035        self.clockWd = None  # used in TOF
2036        self.ReInitialize()
2037
2038    def ReInitialize(self):
2039        'Reinitialize the Reader to initial settings'
2040        ImportBaseclass.ReInitialize(self)
2041        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2042        self.powderdata = [] # Powder dataset
2043        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2044                np.array(x), # x-axis values
2045                np.array(y), # powder pattern intensities
2046                np.array(w), # 1/sig(intensity)^2 values (weights)
2047                np.array(yc), # calc. intensities (zero)
2048                np.array(yb), # calc. background (zero)
2049                np.array(yd), # obs-calc profiles
2050        '''
2051        self.comments = []
2052        self.idstring = ''
2053        self.Sample = SetDefaultSample() # default sample parameters
2054        self.Controls = {}  # items to be placed in top-level Controls
2055        self.GSAS = None     # used in TOF
2056        self.repeat_instparm = True # Should a parm file be
2057        #                             used for multiple histograms?
2058        self.instparm = None # name hint from file of instparm to use
2059        self.instfile = '' # full path name to instrument parameter file
2060        self.instbank = '' # inst parm bank number
2061        self.instmsg = ''  # a label that gets printed to show
2062                           # where instrument parameters are from
2063        self.numbanks = 1
2064        self.instdict = {} # place items here that will be transferred to the instrument parameters
2065        self.pwdparms = {} # place parameters that are transferred directly to the tree
2066                           # here (typically from an existing GPX file)
2067######################################################################
2068class ImportSmallAngleData(ImportBaseclass):
2069    '''Defines a base class for the reading of files with small angle data.
2070    See :ref:`Writing a Import Routine<Import_Routines>`
2071    for an explanation on how to use this class.
2072    '''
2073    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2074        strictExtension=False,):
2075
2076        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2077            strictExtension)
2078        self.ReInitialize()
2079
2080    def ReInitialize(self):
2081        'Reinitialize the Reader to initial settings'
2082        ImportBaseclass.ReInitialize(self)
2083        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2084        self.smallangledata = [] # SASD dataset
2085        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2086                np.array(x), # x-axis values
2087                np.array(y), # powder pattern intensities
2088                np.array(w), # 1/sig(intensity)^2 values (weights)
2089                np.array(yc), # calc. intensities (zero)
2090                np.array(yd), # obs-calc profiles
2091                np.array(yb), # preset bkg
2092        '''
2093        self.comments = []
2094        self.idstring = ''
2095        self.Sample = SetDefaultSample()
2096        self.GSAS = None     # used in TOF
2097        self.clockWd = None  # used in TOF
2098        self.numbanks = 1
2099        self.instdict = {} # place items here that will be transferred to the instrument parameters
2100
2101######################################################################
2102class ImportReflectometryData(ImportBaseclass):
2103    '''Defines a base class for the reading of files with reflectometry data.
2104    See :ref:`Writing a Import Routine<Import_Routines>`
2105    for an explanation on how to use this class.
2106    '''
2107    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2108        strictExtension=False,):
2109
2110        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2111            strictExtension)
2112        self.ReInitialize()
2113
2114    def ReInitialize(self):
2115        'Reinitialize the Reader to initial settings'
2116        ImportBaseclass.ReInitialize(self)
2117        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2118        self.reflectometrydata = [] # SASD dataset
2119        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2120                np.array(x), # x-axis values
2121                np.array(y), # powder pattern intensities
2122                np.array(w), # 1/sig(intensity)^2 values (weights)
2123                np.array(yc), # calc. intensities (zero)
2124                np.array(yd), # obs-calc profiles
2125                np.array(yb), # preset bkg
2126        '''
2127        self.comments = []
2128        self.idstring = ''
2129        self.Sample = SetDefaultSample()
2130        self.GSAS = None     # used in TOF
2131        self.clockWd = None  # used in TOF
2132        self.numbanks = 1
2133        self.instdict = {} # place items here that will be transferred to the instrument parameters
2134
2135######################################################################
2136class ImportPDFData(ImportBaseclass):
2137    '''Defines a base class for the reading of files with PDF G(R) data.
2138    See :ref:`Writing a Import Routine<Import_Routines>`
2139    for an explanation on how to use this class.
2140    '''
2141    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2142        strictExtension=False,):
2143
2144        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2145            strictExtension)
2146        self.ReInitialize()
2147
2148    def ReInitialize(self):
2149        'Reinitialize the Reader to initial settings'
2150        ImportBaseclass.ReInitialize(self)
2151        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2152        self.pdfdata = [] # PDF G(R) dataset
2153        '''A pdf g(r) data set is a list with items [x,y]:
2154                np.array(x), # r-axis values
2155                np.array(y), # pdf g(r)
2156        '''
2157        self.comments = []
2158        self.idstring = ''
2159        self.numbanks = 1
2160
2161######################################################################
2162class ImportImage(ImportBaseclass):
2163    '''Defines a base class for the reading of images
2164
2165    Images are read in only these places:
2166
2167      * Initial reading is typically done from a menu item
2168        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2169        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2170        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2171        :meth:`Reader`. This returns a list of reader objects for each read image.
2172
2173      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2174        directly into the data tree.
2175
2176      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2177
2178    .. _Image_import_routines:
2179
2180    When reading an image, the ``Reader()`` routine in the ImportImage class
2181    should set:
2182
2183      * :attr:`Comments`: a list of strings (str),
2184      * :attr:`Npix`: the number of pixels in the image (int),
2185      * :attr:`Image`: the actual image as a numpy array (np.array)
2186      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2187        data items are needed:
2188
2189         * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2190         * 'wavelength': wavelength in Angstoms.
2191         * 'distance': distance of detector from sample in cm.
2192         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2193         * 'size': size of image (such as ``[2048,2048]``).
2194         * 'ImageTag': image number or other keyword used to retrieve image from
2195           a multi-image data file (defaults to ``1`` if not specified).
2196         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2197
2198    optional data items:
2199
2200      * :attr:`repeat`: set to True if there are additional images to
2201        read in the file, False otherwise
2202      * :attr:`repeatcount`: set to the number of the image.
2203
2204    Note that the above is initialized with :meth:`InitParameters`.
2205    (Also see :ref:`Writing a Import Routine<Import_Routines>`
2206    for an explanation on how to use import classes in general.)
2207    '''
2208    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2209        strictExtension=False,):
2210        ImportBaseclass.__init__(self,formatName,longFormatName,
2211            extensionlist,strictExtension)
2212        self.InitParameters()
2213
2214    def ReInitialize(self):
2215        'Reinitialize the Reader to initial settings -- not used at present'
2216        ImportBaseclass.ReInitialize(self)
2217        self.InitParameters()
2218
2219    def InitParameters(self):
2220        'initialize the instrument parameters structure'
2221        self.Comments = ['No comments']
2222        self.Data = {}
2223        self.Npix = 0
2224        self.Image = None
2225        self.repeat = False
2226        self.repeatcount = 1
2227        self.sumfile = ''
2228
2229    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2230        '''Optionally, call this after reading in an image to load it into the tree.
2231        This saves time by preventing a reread of the same information.
2232        '''
2233        if ParentFrame:
2234            ParentFrame.ImageZ = self.Image   # store the image for plotting
2235            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2236            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2237
2238#################################################################################################
2239# shortcut routines
2240exp = np.exp
2241sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2242cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2243tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2244sqrt = sq = lambda x: np.sqrt(x)
2245pi = lambda: np.pi
2246class ExpressionObj(object):
2247    '''Defines an object with a user-defined expression, to be used for
2248    secondary fits or restraints. Object is created null, but is changed
2249    using :meth:`LoadExpression`. This contains only the minimum
2250    information that needs to be stored to save and load the expression
2251    and how it is mapped to GSAS-II variables.
2252    '''
2253    def __init__(self):
2254        self.expression = ''
2255        'The expression as a text string'
2256        self.assgnVars = {}
2257        '''A dict where keys are label names in the expression mapping to a GSAS-II
2258        variable. The value a G2 variable name.
2259        Note that the G2 variable name may contain a wild-card and correspond to
2260        multiple values.
2261        '''
2262        self.freeVars = {}
2263        '''A dict where keys are label names in the expression mapping to a free
2264        parameter. The value is a list with:
2265
2266         * a name assigned to the parameter
2267         * a value for to the parameter and
2268         * a flag to determine if the variable is refined.
2269        '''
2270        self.depVar = None
2271
2272        self.lastError = ('','')
2273        '''Shows last encountered error in processing expression
2274        (list of 1-3 str values)'''
2275
2276        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2277        self.distance_atoms = None  # to be used for defining atom distances
2278
2279    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2280        '''Load the expression and associated settings into the object. Raises
2281        an exception if the expression is not parsed, if not all functions
2282        are defined or if not all needed parameter labels in the expression
2283        are defined.
2284
2285        This will not test if the variable referenced in these definitions
2286        are actually in the parameter dictionary. This is checked when the
2287        computation for the expression is done in :meth:`SetupCalc`.
2288
2289        :param str expr: the expression
2290        :param list exprVarLst: parameter labels found in the expression
2291        :param dict varSelect: this will be 0 for Free parameters
2292          and non-zero for expression labels linked to G2 variables.
2293        :param dict varName: Defines a name (str) associated with each free parameter
2294        :param dict varValue: Defines a value (float) associated with each free parameter
2295        :param dict varRefflag: Defines a refinement flag (bool)
2296          associated with each free parameter
2297        '''
2298        self.expression = expr
2299        self.compiledExpr = None
2300        self.freeVars = {}
2301        self.assgnVars = {}
2302        for v in exprVarLst:
2303            if varSelect[v] == 0:
2304                self.freeVars[v] = [
2305                    varName.get(v),
2306                    varValue.get(v),
2307                    varRefflag.get(v),
2308                    ]
2309            else:
2310                self.assgnVars[v] = varName[v]
2311        self.CheckVars()
2312
2313    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2314        '''Load the expression and associated settings from the object into
2315        arrays used for editing.
2316
2317        :param list exprVarLst: parameter labels found in the expression
2318        :param dict varSelect: this will be 0 for Free parameters
2319          and non-zero for expression labels linked to G2 variables.
2320        :param dict varName: Defines a name (str) associated with each free parameter
2321        :param dict varValue: Defines a value (float) associated with each free parameter
2322        :param dict varRefflag: Defines a refinement flag (bool)
2323          associated with each free parameter
2324
2325        :returns: the expression as a str
2326        '''
2327        for v in self.freeVars:
2328            varSelect[v] = 0
2329            varName[v] = self.freeVars[v][0]
2330            varValue[v] = self.freeVars[v][1]
2331            varRefflag[v] = self.freeVars[v][2]
2332        for v in self.assgnVars:
2333            varSelect[v] = 1
2334            varName[v] = self.assgnVars[v]
2335        return self.expression
2336
2337    def GetVaried(self):
2338        'Returns the names of the free parameters that will be refined'
2339        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
2340
2341    def GetVariedVarVal(self):
2342        'Returns the names and values of the free parameters that will be refined'
2343        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
2344
2345    def UpdateVariedVars(self,varyList,values):
2346        'Updates values for the free parameters (after a refinement); only updates refined vars'
2347        for v in self.freeVars:
2348            if not self.freeVars[v][2]: continue
2349            if "::"+self.freeVars[v][0] not in varyList: continue
2350            indx = varyList.index("::"+self.freeVars[v][0])
2351            self.freeVars[v][1] = values[indx]
2352
2353    def GetIndependentVars(self):
2354        'Returns the names of the required independent parameters used in expression'
2355        return [self.assgnVars[v] for v in self.assgnVars]
2356
2357    def CheckVars(self):
2358        '''Check that the expression can be parsed, all functions are
2359        defined and that input loaded into the object is internally
2360        consistent. If not an Exception is raised.
2361
2362        :returns: a dict with references to packages needed to
2363          find functions referenced in the expression.
2364        '''
2365        ret = self.ParseExpression(self.expression)
2366        if not ret:
2367            raise Exception("Expression parse error")
2368        exprLblList,fxnpkgdict = ret
2369        # check each var used in expression is defined
2370        defined = self.assgnVars.keys() + self.freeVars.keys()
2371        notfound = []
2372        for var in exprLblList:
2373            if var not in defined:
2374                notfound.append(var)
2375        if notfound:
2376            msg = 'Not all variables defined'
2377            msg1 = 'The following variables were not defined: '
2378            msg2 = ''
2379            for var in notfound:
2380                if msg: msg += ', '
2381                msg += var
2382            self.lastError = (msg1,'  '+msg2)
2383            raise Exception(msg)
2384        return fxnpkgdict
2385
2386    def ParseExpression(self,expr):
2387        '''Parse an expression and return a dict of called functions and
2388        the variables used in the expression. Returns None in case an error
2389        is encountered. If packages are referenced in functions, they are loaded
2390        and the functions are looked up into the modules global
2391        workspace.
2392
2393        Note that no changes are made to the object other than
2394        saving an error message, so that this can be used for testing prior
2395        to the save.
2396
2397        :returns: a list of used variables
2398        '''
2399        self.lastError = ('','')
2400        import ast
2401        def FindFunction(f):
2402            '''Find the object corresponding to function f
2403            :param str f: a function name such as 'numpy.exp'
2404            :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2405              that defines the package location(s) and where pkgobj
2406              defines the object associated with the function.
2407              If the function is not found, pkgobj is None.
2408            '''
2409            df = f.split('.')
2410            pkgdict = {}
2411            # no listed package, try in current namespace
2412            if len(df) == 1:
2413                try:
2414                    fxnobj = eval(f)
2415                    return pkgdict,fxnobj
2416                except (AttributeError, NameError):
2417                    return None,None
2418            else:
2419                try:
2420                    fxnobj = eval(f)
2421                    pkgdict[df[0]] = eval(df[0])
2422                    return pkgdict,fxnobj
2423                except (AttributeError, NameError):
2424                    pass
2425            # includes a package, lets try to load the packages
2426            pkgname = ''
2427            path = sys.path+['./',]
2428            for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2429                if pkgname:
2430                    pkgname += '.' + pkg
2431                else:
2432                    pkgname = pkg
2433                fp = None
2434                try:
2435                    fp, fppath,desc = imp.find_module(pkg,path)
2436                    pkgobj = imp.load_module(pkg,fp,fppath,desc)
2437                    pkgdict[pkgname] = pkgobj
2438                    path = [fppath]
2439                except Exception as msg:
2440                    print('load of '+pkgname+' failed with error='+str(msg))
2441                    return {},None
2442                finally:
2443                    if fp: fp.close()
2444                try:
2445                    #print 'before',pkgdict.keys()
2446                    fxnobj = eval(f,globals(),pkgdict)
2447                    #print 'after 1',pkgdict.keys()
2448                    #fxnobj = eval(f,pkgdict)
2449                    #print 'after 2',pkgdict.keys()
2450                    return pkgdict,fxnobj
2451                except:
2452                    continue
2453            return None # not found
2454        def ASTtransverse(node,fxn=False):
2455            '''Transverse a AST-parsed expresson, compiling a list of variables
2456            referenced in the expression. This routine is used recursively.
2457
2458            :returns: varlist,fxnlist where
2459              varlist is a list of referenced variable names and
2460              fxnlist is a list of used functions
2461            '''
2462            varlist = []
2463            fxnlist = []
2464            if isinstance(node, list):
2465                for b in node:
2466                    v,f = ASTtransverse(b,fxn)
2467                    varlist += v
2468                    fxnlist += f
2469            elif isinstance(node, ast.AST):
2470                for a, b in ast.iter_fields(node):
2471                    if isinstance(b, ast.AST):
2472                        if a == 'func':
2473                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
2474                            continue
2475                        v,f = ASTtransverse(b,fxn)
2476                        varlist += v
2477                        fxnlist += f
2478                    elif isinstance(b, list):
2479                        v,f = ASTtransverse(b,fxn)
2480                        varlist += v
2481                        fxnlist += f
2482                    elif node.__class__.__name__ == "Name":
2483                        varlist += [b]
2484                    elif fxn and node.__class__.__name__ == "Attribute":
2485                        varlist += [b]
2486            return varlist,fxnlist
2487        try:
2488            exprast = ast.parse(expr)
2489        except SyntaxError:
2490            s = ''
2491            import traceback
2492            for i in traceback.format_exc().splitlines()[-3:-1]:
2493                if s: s += "\n"
2494                s += str(i)
2495            self.lastError = ("Error parsing expression:",s)
2496            return
2497        # find the variables & functions
2498        v,f = ASTtransverse(exprast)
2499        varlist = sorted(list(set(v)))
2500        fxnlist = list(set(f))
2501        pkgdict = {}
2502        # check the functions are defined
2503        for fxn in fxnlist:
2504            fxndict,fxnobj = FindFunction(fxn)
2505            if not fxnobj:
2506                self.lastError = ("Error: Invalid function",fxn,
2507                                  "is not defined")
2508                return
2509            if not hasattr(fxnobj,'__call__'):
2510                self.lastError = ("Error: Not a function.",fxn,
2511                                  "cannot be called as a function")
2512                return
2513            pkgdict.update(fxndict)
2514        return varlist,pkgdict
2515
2516    def GetDepVar(self):
2517        'return the dependent variable, or None'
2518        return self.depVar
2519
2520    def SetDepVar(self,var):
2521        'Set the dependent variable, if used'
2522        self.depVar = var
2523#==========================================================================
2524class ExpressionCalcObj(object):
2525    '''An object used to evaluate an expression from a :class:`ExpressionObj`
2526    object.
2527
2528    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
2529      an expression string and mappings for the parameter labels in that object.
2530    '''
2531    def __init__(self,exprObj):
2532        self.eObj = exprObj
2533        'The expression and mappings; a :class:`ExpressionObj` object'
2534        self.compiledExpr = None
2535        'The expression as compiled byte-code'
2536        self.exprDict = {}
2537        '''dict that defines values for labels used in expression and packages
2538        referenced by functions
2539        '''
2540        self.lblLookup = {}
2541        '''Lookup table that specifies the expression label name that is
2542        tied to a particular GSAS-II parameters in the parmDict.
2543        '''
2544        self.fxnpkgdict = {}
2545        '''a dict with references to packages needed to
2546        find functions referenced in the expression.
2547        '''
2548        self.varLookup = {}
2549        '''Lookup table that specifies the GSAS-II variable(s)
2550        indexed by the expression label name. (Used for only for diagnostics
2551        not evaluation of expression.)
2552        '''
2553        self.su = None
2554        '''Standard error evaluation where supplied by the evaluator
2555        '''
2556        # Patch: for old-style expressions with a (now removed step size)
2557        for v in self.eObj.assgnVars:
2558            if not isinstance(self.eObj.assgnVars[v], basestring):
2559                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
2560        self.parmDict = {}
2561        '''A copy of the parameter dictionary, for distance and angle computation
2562        '''
2563
2564    def SetupCalc(self,parmDict):
2565        '''Do all preparations to use the expression for computation.
2566        Adds the free parameter values to the parameter dict (parmDict).
2567        '''
2568        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2569            return
2570        self.fxnpkgdict = self.eObj.CheckVars()
2571        # all is OK, compile the expression
2572        self.compiledExpr = compile(self.eObj.expression,'','eval')
2573
2574        # look at first value in parmDict to determine its type
2575        parmsInList = True
2576        for key in parmDict:
2577            val = parmDict[key]
2578            if isinstance(val, basestring):
2579                parmsInList = False
2580                break
2581            try: # check if values are in lists
2582                val = parmDict[key][0]
2583            except (TypeError,IndexError):
2584                parmsInList = False
2585            break
2586
2587        # set up the dicts needed to speed computations
2588        self.exprDict = {}
2589        self.lblLookup = {}
2590        self.varLookup = {}
2591        for v in self.eObj.freeVars:
2592            varname = self.eObj.freeVars[v][0]
2593            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
2594            self.lblLookup[varname] = v
2595            self.varLookup[v] = varname
2596            if parmsInList:
2597                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
2598            else:
2599                parmDict[varname] = self.eObj.freeVars[v][1]
2600            self.exprDict[v] = self.eObj.freeVars[v][1]
2601        for v in self.eObj.assgnVars:
2602            varname = self.eObj.assgnVars[v]
2603            if '*' in varname:
2604                varlist = LookupWildCard(varname,list(parmDict.keys()))
2605                if len(varlist) == 0:
2606                    raise Exception("No variables match "+str(v))
2607                for var in varlist:
2608                    self.lblLookup[var] = v
2609                if parmsInList:
2610                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
2611                else:
2612                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
2613                self.varLookup[v] = [var for var in varlist]
2614            elif varname in parmDict:
2615                self.lblLookup[varname] = v
2616                self.varLookup[v] = varname
2617                if parmsInList:
2618                    self.exprDict[v] = parmDict[varname][0]
2619                else:
2620                    self.exprDict[v] = parmDict[varname]
2621            else:
2622                self.exprDict[v] = None
2623#                raise Exception,"No value for variable "+str(v)
2624        self.exprDict.update(self.fxnpkgdict)
2625
2626    def UpdateVars(self,varList,valList):
2627        '''Update the dict for the expression with a set of values
2628        :param list varList: a list of variable names
2629        :param list valList: a list of corresponding values
2630        '''
2631        for var,val in zip(varList,valList):
2632            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
2633
2634    def UpdateDict(self,parmDict):
2635        '''Update the dict for the expression with values in a dict
2636        :param list parmDict: a dict of values some of which may be in use here
2637        '''
2638        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2639            self.parmDict = parmDict
2640            return
2641        for var in parmDict:
2642            if var in self.lblLookup:
2643                self.exprDict[self.lblLookup[var]] = parmDict[var]
2644
2645    def EvalExpression(self):
2646        '''Evaluate an expression. Note that the expression
2647        and mapping are taken from the :class:`ExpressionObj` expression object
2648        and the parameter values were specified in :meth:`SetupCalc`.
2649        :returns: a single value for the expression. If parameter
2650        values are arrays (for example, from wild-carded variable names),
2651        the sum of the resulting expression is returned.
2652
2653        For example, if the expression is ``'A*B'``,
2654        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
2655
2656        [0.5, 1, 0.5]
2657
2658        then the result will be ``4.0``.
2659        '''
2660        self.su = None
2661        if self.eObj.expression.startswith('Dist'):
2662#            GSASIIpath.IPyBreak()
2663            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
2664            return dist
2665        elif self.eObj.expression.startswith('Angle'):
2666            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
2667            return angle
2668        if self.compiledExpr is None:
2669            raise Exception("EvalExpression called before SetupCalc")
2670        try:
2671            val = eval(self.compiledExpr,globals(),self.exprDict)
2672        except TypeError:
2673            val = None
2674        if not np.isscalar(val):
2675            val = np.sum(val)
2676        return val
2677
2678class G2Exception(Exception):
2679    def __init__(self,msg):
2680        self.msg = msg
2681    def __str__(self):
2682        return repr(self.msg)
2683
2684def HowDidIgetHere(wherecalledonly=False):
2685    '''Show a traceback with calls that brought us to the current location.
2686    Used for debugging.
2687    '''
2688    import traceback
2689    if wherecalledonly:
2690        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
2691        print(i.strip().rstrip())
2692    else:
2693        print (70*'*')
2694        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
2695        print (70*'*')
2696
2697def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
2698    '''Create and initialize a new set of PDF tree entries
2699
2700    :param Frame G2frame: main GSAS-II tree frame object
2701    :param str PWDRtree: name of PWDR to be used to create PDF item
2702    :param dict ElList: data structure with composition
2703    :param list Qlimits: Q limits to be used for computing the PDF
2704    :param float numAtm: no. atom in chemical formula
2705    :param float FltBkg: flat background value
2706    :param list PDFnames: previously used PDF names
2707
2708    :returns: the Id of the newly created PDF entry
2709    '''
2710    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
2711    if PDFname in PDFnames:
2712        print('Skipping, entry already exists: '+PDFname)
2713        return None
2714    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
2715    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
2716    Data = {
2717        'Sample':{'Name':PWDRtree,'Mult':1.0},
2718        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
2719        'Container':{'Name':'','Mult':-1.0,'Refine':False},
2720        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
2721        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
2722        'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
2723        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,
2724        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
2725    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
2726    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
2727        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
2728    return Id
2729
2730class ShowTiming(object):
2731    '''An object to use for timing repeated sections of code.
2732
2733    Create the object with::
2734       tim0 = ShowTiming()
2735
2736    Tag sections of code to be timed with::
2737       tim0.start('start')
2738       tim0.start('in section 1')
2739       tim0.start('in section 2')
2740    etc. (Note that each section should have a unique label.)
2741
2742    After the last section, end timing with::
2743       tim0.end()
2744
2745    Show timing results with::
2746       tim0.show()
2747       
2748    '''
2749    import time
2750    def __init__(self):
2751        self.timeSum =  []
2752        self.timeStart = []
2753        self.label = []
2754        self.prev = None
2755    def start(self,label):
2756        if label in self.label:
2757            i = self.label.index(label)
2758            self.timeStart[i] = time.time()
2759        else:
2760            i = len(self.label)
2761            self.timeSum.append(0.0)
2762            self.timeStart.append(time.time())
2763            self.label.append(label)
2764        if self.prev is not None:
2765            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
2766        self.prev = i
2767    def end(self):
2768        if self.prev is not None:
2769            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
2770        self.prev = None
2771    def show(self):
2772        sumT = sum(self.timeSum)
2773        print('Timing results (total={:.2f} sec)'.format(sumT))
2774        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
2775            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
2776
2777
2778if __name__ == "__main__":
2779    # test equation evaluation
2780    def showEQ(calcobj):
2781        print (50*'=')
2782        print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
2783        for v in sorted(calcobj.varLookup):
2784            print ("  "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
2785        # print '  Derivatives'
2786        # for v in calcobj.derivStep.keys():
2787        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
2788
2789    obj = ExpressionObj()
2790
2791    obj.expression = "A*np.exp(B)"
2792    obj.assgnVars =  {'B': '0::Afrac:1'}
2793    obj.freeVars =  {'A': [u'A', 0.5, True]}
2794    #obj.CheckVars()
2795    calcobj = ExpressionCalcObj(obj)
2796
2797    obj1 = ExpressionObj()
2798    obj1.expression = "A*np.exp(B)"
2799    obj1.assgnVars =  {'B': '0::Afrac:*'}
2800    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
2801    #obj.CheckVars()
2802    calcobj1 = ExpressionCalcObj(obj1)
2803
2804    obj2 = ExpressionObj()
2805    obj2.distance_stuff = np.array([[0,1],[1,-1]])
2806    obj2.expression = "Dist(1,2)"
2807    GSASIIpath.InvokeDebugOpts()
2808    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
2809    calcobj2 = ExpressionCalcObj(obj2)
2810    calcobj2.SetupCalc(parmDict2)
2811    showEQ(calcobj2)
2812
2813    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
2814    print ('\nDict = '+parmDict1)
2815    calcobj.SetupCalc(parmDict1)
2816    showEQ(calcobj)
2817    calcobj1.SetupCalc(parmDict1)
2818    showEQ(calcobj1)
2819
2820    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
2821    print ('Dict = '+parmDict2)
2822    calcobj.SetupCalc(parmDict2)
2823    showEQ(calcobj)
2824    calcobj1.SetupCalc(parmDict2)
2825    showEQ(calcobj1)
2826    calcobj2.SetupCalc(parmDict2)
2827    showEQ(calcobj2)
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