source: trunk/GSASIIobj.py @ 4399

Last change on this file since 4399 was 4399, checked in by toby, 20 months ago

major refactoring & corrections to ISODISTORT mode import and computations

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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2020-04-13 01:46:57 +0000 (Mon, 13 Apr 2020) $
5# $Author: toby $
6# $Revision: 4399 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 4399 2020-04-13 01:46:57Z toby $
9########### SVN repository information ###################
10
11'''
12*GSASIIobj: Data objects*
13=========================
14
15This module defines and/or documents the data structures used in GSAS-II, as well
16as provides misc. support routines.
17
18.. Next command allows \AA to be used in HTML
19
20.. only:: html
21
22   :math:`\\require{mediawiki-texvc}`
23
24.. _Constraints_table:
25
26.. index::
27   single: Constraints object description
28   single: Data object descriptions; Constraints
29
30Constraints Tree Item
31----------------------
32
33Constraints are stored in a dict, separated into groups.
34Note that parameter are named in the following pattern,
35p:h:<var>:n, where p is the phase number, h is the histogram number
36<var> is a variable name and n is the parameter number.
37If a parameter does not depend on a histogram or phase or is unnumbered, that
38number is omitted.
39Note that the contents of each dict item is a List where each element in the
40list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
41The constraints in this form are converted in
42:func:`GSASIIstrIO.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
43
44The keys in the Constraints dict are:
45
46.. tabularcolumns:: |l|p{4.5in}|
47
48==========  ====================================================
49  key         explanation
50==========  ====================================================
51Hist        This specifies a list of constraints on
52            histogram-related parameters,
53            which will be of form :h:<var>:n.
54HAP         This specifies a list of constraints on parameters
55            that are defined for every histogram in each phase
56            and are of form p:h:<var>:n.
57Phase       This specifies a list of constraints on phase
58            parameters,
59            which will be of form p::<var>:n.
60Global      This specifies a list of constraints on parameters
61            that are not tied to a histogram or phase and
62            are of form ::<var>:n
63==========  ====================================================
64
65.. _Constraint_definitions_table:
66
67.. index::
68   single: Constraint definition object description
69   single: Data object descriptions; Constraint Definition
70
71Each constraint is defined as an item in a list. Each constraint is of form::
72
73[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
74
75Where the variable pair list item containing two values [<mult>, <var>], where:
76
77  * <mult> is a multiplier for the constraint (float)
78  * <var> a :class:`G2VarObj` object (previously a str variable name of form
79      'p:h:name[:at]')
80
81Note that the last three items in the list play a special role:
82
83 * <fixedval> is the fixed value for a `constant equation` (``constype=c``)
84   constraint or is None. For a `New variable` (``constype=f``) constraint,
85   a variable name can be specified as a str (used for externally
86   generated constraints)
87 * <varyflag> is True or False for `New variable` (``constype=f``) constraints
88   or is None. This indicates if this variable should be refined.
89 * <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
90
91    * 'e' defines a set of equivalent variables. Only the first variable is refined (if the
92      appropriate refine flag is set) and and all other equivalent variables in the list
93      are generated from that variable, using the appropriate multipliers.
94    * 'c' defines a constraint equation of form,
95      :math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
96    * 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
97      even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
98      constraint and the mult value is ignored.
99      This is of particular value when needing to hold one or more variables where a
100      single flag controls a set of variables such as, coordinates,
101      the reciprocal metric tensor or anisotropic displacement parameter.
102    * 'f' defines a new variable (function) according to relationship
103      :math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
104
105.. _Covariance_table:
106
107.. index::
108   single: Covariance description
109   single: Data object descriptions; Covariance
110
111Covariance Tree Item
112--------------------
113
114The Covariance tree item has results from the last least-squares run. They
115are stored in a dict with these keys:
116
117.. tabularcolumns:: |l|l|p{4in}|
118
119=============  ===============  ====================================================
120  key            sub-key        explanation
121=============  ===============  ====================================================
122newCellDict    \                (dict) ith lattice parameters computed by
123                                :func:`GSASIIstrMath.GetNewCellParms`
124title          \                (str) Name of gpx file(?)
125variables      \                (list) Values for all N refined variables
126                                (list of float values, length N,
127                                ordered to match varyList)
128sig            \                (list) Uncertainty values for all N refined variables
129                                (list of float values, length N,
130                                ordered to match varyList)
131varyList       \                (list of str values, length N) List of directly refined variables
132                               
133newAtomDict    \                (dict) atom position values computed in
134                                :func:`GSASIIstrMath.ApplyXYZshifts`
135Rvals          \                (dict) R-factors, GOF, Marquardt value for last
136                                refinement cycle
137\              Nobs             (int) Number of observed data points
138\              Rwp              (float) overall weighted profile R-factor (%)
139\              chisq            (float) :math:`\sum w*(I_{obs}-I_{calc})^2`                               
140                                for all data.
141                                Note: this is not the reduced :math:`\chi^2`.
142\              lamMax           (float) Marquardt value applied to Hessian diagonal
143\              GOF              (float) The goodness-of-fit, aka square root of
144                                the reduced chi squared.
145covMatrix      \                (np.array) The (NxN) covVariance matrix
146=============  ===============  ====================================================
147
148.. _Phase_table:
149
150.. index::
151   single: Phase object description
152   single: Data object descriptions; Phase
153
154Phase Tree Items
155----------------
156
157Phase information is stored in the GSAS-II data tree as children of the
158Phases item in a dict with keys:
159
160.. tabularcolumns:: |l|l|p{4in}|
161
162==========  ===============     =====================================================================================================
163  key         sub-key           explanation
164==========  ===============     =====================================================================================================
165General         \               (dict) Overall information for the phase
166  \         3Dproj              (list of str) projections for 3D pole distribution plots
167  \         AngleRadii          (list of floats) Default radius for each atom used to compute
168                                interatomic angles
169  \         AtomMass            (list of floats) Masses for atoms
170  \         AtomPtrs            (list of int) four locations (cx,ct,cs & cu) to use to pull info
171                                from the atom records
172  \         AtomTypes           (llist of str) Atom types
173  \         BondRadii           (list of floats) Default radius for each atom used to compute
174                                interatomic distances
175  \         Cell                Unit cell parameters & ref. flag
176                                (list with 8 items. All but first item are float.)
177
178                                 0: cell refinement flag (True/False),
179                                 1-3: a, b, c, (:math:`\\AA`)
180                                 4-6: alpha, beta & gamma, (degrees)
181                                 7: volume (:math:`\\AA^3`)
182  \         Color               (list of (r,b,g) triplets) Colors for atoms
183  \         Compare             (dict) Polygon comparison parameters
184  \         Data plot type      (str) data plot type ('Mustrain', 'Size' or
185                                'Preferred orientation') for powder data
186  \         DisAglCtls          (dDict) with distance/angle search controls,
187                                which has keys 'Name', 'AtomTypes',
188                                'BondRadii', 'AngleRadii' which are as above
189                                except are possibly edited. Also contains
190                                'Factors', which is a 2 element list with
191                                a multiplier for bond and angle search range
192                                [typically (0.85,0.85)].
193  \         F000X               (float) x-ray F(000) intensity
194  \         F000N               (float) neutron F(000) intensity
195  \         Flip                (dict) Charge flip controls
196  \         HydIds              (dict) geometrically generated hydrogen atoms
197  \         Isotope             (dict) Isotopes for each atom type
198  \         Isotopes            (dict) Scattering lengths for each isotope
199                                combination for each element in phase
200  \         MCSA controls       (dict) Monte Carlo-Simulated Annealing controls
201  \         Map                 (dict) Map parameters
202  \         Mass                (float) Mass of unit cell contents in g/mol
203  \         Modulated           (bool) True if phase modulated
204  \         Mydir               (str) Directory of current .gpx file
205  \         Name                (str) Phase name
206  \         NoAtoms             (dict) Number of atoms per unit cell of each type
207  \         POhkl               (list) March-Dollase preferred orientation direction
208  \         Pawley dmin         (float) maximum Q (as d-space) to use for Pawley extraction
209  \         Pawley dmax         (float) minimum Q (as d-space) to use for Pawley extraction
210  \         Pawley neg wt       (float) Restraint value for negative Pawley intensities
211  \         SGData              (object) Space group details as a
212                                :ref:`space group (SGData) <SGData_table>`
213                                object, as defined in :func:`GSASIIspc.SpcGroup`.
214  \         SH Texture          (dict) Spherical harmonic preferred orientation parameters
215  \         Super               (int) dimension of super group (0,1 only)
216  \         Type                (str) phase type (e.g. 'nuclear')
217  \         Z                   (dict) Atomic numbers for each atom type
218  \         doDysnomia          (bool) flag for max ent map modification via Dysnomia
219  \         doPawley            (bool) Flag for Pawley intensity extraction
220  \         vdWRadii            (dict) Van der Waals radii for each atom type
221ranId           \               (int) unique random number Id for phase
222pId             \               (int) Phase Id number for current project.
223Atoms           \               (list of lists) Atoms in phase as a list of lists. The outer list
224                                is for each atom, the inner list contains varying
225                                items depending on the type of phase, see
226                                the :ref:`Atom Records <Atoms_table>` description.
227Drawing         \               (dict) Display parameters
228\           Atoms               (list of lists) with an entry for each atom that is drawn
229\           Plane               (list) Controls for contour density plane display
230\           Quaternion          (4 element np.array) Viewing quaternion
231\           Zclip               (float) clipping distance in :math:`\\AA`
232\           Zstep               (float) Step to de/increase Z-clip
233\           atomPtrs            (list) positions of x, type, site sym, ADP flag in Draw Atoms
234\           backColor           (list) background for plot as and R,G,B triplet
235                                (default = [0, 0, 0], black).
236\           ballScale           (float) Radius of spheres in ball-and-stick display
237\           bondList            (dict) Bonds
238\           bondRadius          (float) Radius of binds in :math:`\\AA`
239\           cameraPos           (float) Viewing position in :math:`\\AA` for plot
240\           contourLevel        (float) map contour level in :math:`e/\\AA^3`
241\           contourMax          (float) map contour maximum
242\           depthFog            (bool) True if use depthFog on plot - set currently as False
243\           ellipseProb         (float) Probability limit for display of thermal
244                                ellipsoids in % .
245\           magMult             (float) multiplier for magnetic moment arrows
246\           mapSize             (float) x & y dimensions of contourmap (fixed internally)
247\           modelView           (4,4 array) from openGL drawing transofmation matrix
248\           oldxy               (list with two floats) previous view point
249\           radiusFactor        (float) Distance ratio for searching for bonds. Bonds
250                                are located that are within r(Ra+Rb) and (Ra+Rb)/r
251                                where Ra and Rb are the atomic radii.
252\           selectedAtoms       (list of int values) List of selected atoms
253\           showABC             (bool) Flag to show view point triplet. True=show.
254\           showHydrogen        (bool) Flag to control plotting of H atoms.
255\           showRigidBodies     (bool) Flag to highlight rigid body placement
256\           showSlice           (bool) flag to show contour map
257\           sizeH               (float) Size ratio for H atoms
258\           unitCellBox         (bool) Flag to control display of the unit cell.
259\           vdwScale            (float) Multiplier of van der Waals radius for display of vdW spheres.
260\           viewDir             (np.array with three floats) cartesian viewing direction
261\           viewPoint           (list of lists) First item in list is [x,y,z]
262                                in fractional coordinates for the center of
263                                the plot. Second item list of previous & current
264                                atom number viewed (may be [0,0])
265RBModels        \               Rigid body assignments (note Rigid body definitions
266                                are stored in their own main top-level tree entry.)
267RMC             \               (dict) RMCProfile & rmcfull controls
268Pawley ref      \               (list) Pawley reflections
269Histograms      \               (dict of dicts) The key for the outer dict is
270                                the histograms tied to this phase. The inner
271                                dict contains the combined phase/histogram
272                                parameters for items such as scale factors,
273                                size and strain parameters. The following are the
274                                keys to the inner dict. (dict)
275\           Babinet             (dict) For protein crystallography. Dictionary with two
276                                entries, 'BabA', 'BabU'
277\           Extinction          (list of float, bool) Extinction parameter
278\           Flack               (list of [float, bool]) Flack parameter & refine flag
279\           HStrain             (list of two lists) Hydrostatic strain. The first is
280                                a list of the HStrain parameters (1, 2, 3, 4, or 6
281                                depending on unit cell), the second is a list of boolean
282                                refinement parameters (same length)
283\           Histogram           (str) The name of the associated histogram
284\           Layer Disp          (list of [float, bool]) Layer displacement in beam direction & refine flag
285\           LeBail              (bool) Flag for LeBail extraction
286\           Mustrain            (list) Microstrain parameters, in order:
287   
288                                0. Type, one of  u'isotropic', u'uniaxial', u'generalized'
289                                1. Isotropic/uniaxial parameters - list of 3 floats
290                                2. Refinement flags - list of 3 bools
291                                3. Microstrain axis - list of 3 ints, [h, k, l]
292                                4. Generalized mustrain parameters - list of 2-6 floats, depending on space group
293                                5. Generalized refinement flags - list of bools, corresponding to the parameters of (4)
294\           Pref.Ori.           (list) Preferred Orientation. List of eight parameters.
295                                Items marked SH are only used for Spherical Harmonics.
296                               
297                                0. (str) Type, 'MD' for March-Dollase or 'SH' for Spherical Harmonics
298                                1. (float) Value
299                                2. (bool) Refinement flag
300                                3. (list) Preferred direction, list of ints, [h, k, l]
301                                4. (int) SH - number of terms
302                                5. (dict) SH - 
303                                6. (list) SH
304                                7. (float) SH
305\           Scale               (list of [float, bool]) Phase fraction & refine flag
306\           Size                List of crystallite size parameters, in order:
307
308                                0. (str) Type, one of  u'isotropic', u'uniaxial', u'ellipsoidal'
309                                1. (list) Isotropic/uniaxial parameters - list of 3 floats
310                                2. (list) Refinement flags - list of 3 bools
311                                3. (list) Size axis - list of 3 ints, [h, k, l]
312                                4. (list) Ellipsoidal size parameters - list of 6 floats
313                                5. (list) Ellipsoidal refinement flags - list of bools, corresponding to the parameters of (4)
314\           Use                 (bool) True if this histogram is to be used in refinement
315\           newLeBail           (bool) Whether to perform a new LeBail extraction
316MCSA            \               (dict) Monte-Carlo simulated annealing parameters
317==========  ===============     =====================================================================================================
318
319.. _RBData_table:
320
321.. index::
322   single: Rigid Body Data description
323   single: Data object descriptions; Rigid Body Data
324
325Rigid Body Objects
326------------------
327
328Rigid body descriptions are available for two types of rigid bodies: 'Vector'
329and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
330with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
331with defined refinable torsion angles.
332
333.. tabularcolumns:: |l|l|p{4in}|
334
335==========  ===============     ====================================================
336  key         sub-key           explanation
337==========  ===============     ====================================================
338Vector      RBId                (dict of dict) vector rigid bodies
339\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
340\           RBname              (str) Name assigned by user to rigid body
341\           VectMag             (list) vector magnitudes in :math:`\\AA`
342\           rbXYZ               (list of 3 float Cartesian coordinates for Vector rigid body )
343\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
344                                definition, use center of atoms flag
345\           VectRef             (list of bool refinement flags for VectMag values )
346\           rbTypes             (list of str) Atom types for each atom in rigid body
347\           rbVect              (list of lists) Cartesian vectors for each translation used to build rigid body
348\           useCount            (int) Number of times rigid body is used in any structure
349Residue     RBId                (dict of dict) residue rigid bodies
350\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
351\           RBname              (str) Name assigned by user to rigid body
352\           rbXYZ               (list of 3 float) Cartesian coordinates for Residue rigid body
353\           rbTypes             (list of str) Atom types for each atom in rigid body
354\           atNames             (list of str) Names of each atom in rigid body (e.g. C1,N2...)
355\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
356                                definition, use center of atoms flag
357\           rbSeq               (list) Orig,Piv,angle,Riding : definition of internal rigid body
358                                torsion; origin atom (int), pivot atom (int), torsion angle (float),
359                                riding atoms (list of int)
360\           SelSeq              (int,int) used by SeqSizer to identify objects
361\           useCount            (int)Number of times rigid body is used in any structure
362RBIds           \               (dict) unique Ids generated upon creation of each rigid body
363\           Vector              (list) Ids for each Vector rigid body
364\           Residue             (list) Ids for each Residue rigid body
365==========  ===============     ====================================================
366
367.. _SGData_table:
368
369.. index::
370   single: Space Group Data description
371   single: Data object descriptions; Space Group Data
372
373Space Group Objects
374-------------------
375
376Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
377and the information is placed in a SGdata object
378which is a dict with these keys. Magnetic ones are marked "mag"
379
380.. tabularcolumns:: |l|p{4.5in}|
381
382==========  ========================================================================================
383  key         explanation
384==========  ========================================================================================
385BNSlattsym  mag - (str) BNS magnetic space group symbol and centering vector
386GenFlg      mag - (list) symmetry generators indices
387GenSym      mag - (list) names for each generator
388MagMom      mag - (list) "time reversals" for each magnetic operator
389MagPtGp     mag - (str) Magnetic point group symbol
390MagSpGrp    mag - (str) Magnetic space group symbol
391OprNames    mag - (list) names for each space group operation
392SGCen       (np.array) Symmetry cell centering vectors. A (n,3) np.array
393            of centers. Will always have at least one row: ``np.array([[0, 0, 0]])``
394SGFixed     (bool) Only True if phase mported from a magnetic cif file
395            then the space group can not be changed by the user because
396            operator set from cif may be nonstandard
397SGGen       (list) generators
398SGGray      (bool) True if space group is a gray group (incommensurate magnetic structures)
399SGInv       (bool) True if centrosymmetric, False if not
400SGLatt      (str)Lattice centering type. Will be one of
401            P, A, B, C, I, F, R
402SGLaue      (str) one of the following 14 Laue classes:
403            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
404            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m
405SGOps       (list) symmetry operations as a list of form
406            ``[[M1,T1], [M2,T2],...]``
407            where :math:`M_n` is a 3x3 np.array
408            and :math:`T_n` is a length 3 np.array.
409            Atom coordinates are transformed where the
410            Asymmetric unit coordinates [X is (x,y,z)]
411            are transformed using
412            :math:`X^\prime = M_n*X+T_n`
413SGPolax     (str) Axes for space group polarity. Will be one of
414            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
415            'xyz'. In the case where axes are arbitrary
416            '111' is used (P 1, and ?).
417SGPtGrp     (str) Point group of the space group
418SGUniq      unique axis if monoclinic. Will be
419            a, b, or c for monoclinic space groups.
420            Will be blank for non-monoclinic.
421SGSpin      mag - (list) of spin flip operatiors (+1 or -1) for the space group operations
422SGSys       (str) symmetry unit cell: type one of
423            'triclinic', 'monoclinic', 'orthorhombic',
424            'tetragonal', 'rhombohedral', 'trigonal',
425            'hexagonal', 'cubic'
426SSGK1       (list) Superspace multipliers
427SpGrp       (str) space group symbol
428SpnFlp      mag - (list) Magnetic spin flips for every magnetic space group operator
429==========  ========================================================================================
430
431.. _SSGData_table:
432
433.. index::
434   single: Superspace Group Data description
435   single: Data object descriptions; Superspace Group Data
436
437Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
438and the information is placed in a SSGdata object
439which is a dict with these keys:
440
441.. tabularcolumns:: |l|p{4.5in}|
442
443==========  ====================================================
444  key         explanation
445==========  ====================================================
446SSGCen      (list) 4D cell centering vectors [0,0,0,0] at least
447SSGK1       (list) Superspace multipliers
448SSGOps      (list) 4D symmetry operations as [M,T] so that M*x+T = x'
449SSpGrp      (str) superspace group symbol extension to space group
450            symbol, accidental spaces removed
451modQ        (list) modulation/propagation vector
452modSymb     (list of str) Modulation symbols
453==========  ====================================================
454
455
456.. _Atoms_table:
457
458.. index::
459   single: Atoms record description
460   single: Data object descriptions; Atoms record
461
462Atom Records
463------------
464
465If ``phasedict`` points to the phase information in the data tree, then
466atoms are contained in a list of atom records (list) in
467``phasedict['Atoms']``. Also needed to read atom information
468are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
469which define locations in the atom record, as shown below. Items shown are
470always present; additional ones for macromolecular phases are marked 'mm',
471and those for magnetic structures are marked 'mg'
472
473.. tabularcolumns:: |l|p{4.5in}|
474
475==============      ====================================================
476location            explanation
477==============      ====================================================
478ct-4                mm - (str) residue number
479ct-3                mm - (str) residue name (e.g. ALA)
480ct-2                mm - (str) chain label
481ct-1                (str) atom label
482ct                  (str) atom type
483ct+1                (str) refinement flags; combination of 'F', 'X', 'U', 'M'
484cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
485cx+3                (float) site occupancy
486cx+4,cx+5,cx+6      mg - (list) atom magnetic moment along a,b,c in Bohr magnetons
487cs                  (str) site symmetry
488cs+1                (int) site multiplicity
489cia                 (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
490cia+1               (float) Uiso
491cia+2...cia+7       (6 floats) U11, U22, U33, U12, U13, U23
492atom[cia+8]         (int) unique atom identifier
493
494==============      ====================================================
495
496.. _Drawing_atoms_table:
497
498.. index::
499   single: Drawing atoms record description
500   single: Data object descriptions; Drawing atoms record
501
502Drawing Atom Records
503--------------------
504
505If ``phasedict`` points to the phase information in the data tree, then
506drawing atoms are contained in a list of drawing atom records (list) in
507``phasedict['Drawing']['Atoms']``. Also needed to read atom information
508are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
509which define locations in the atom record, as shown below. Items shown are
510always present; additional ones for macromolecular phases are marked 'mm',
511and those for magnetic structures are marked 'mg'
512
513.. tabularcolumns:: |l|p{4.5in}|
514
515==============   ===================================================================================
516location            explanation
517==============   ===================================================================================
518ct-4                mm - (str) residue number
519ct-3                mm - (str) residue name (e.g. ALA)
520ct-2                mm - (str) chain label
521ct-1                (str) atom label
522ct                  (str) atom type
523cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
524cx+3,cx+4,cx+5      mg - (3 floats) atom magnetic moment along a,b,c in Bohr magnetons
525cs-1                (str) Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1')
526cs                  (str) atom drawing style; e.g. 'balls & sticks'
527cs+1                (str) atom label style (e.g. 'name')
528cs+2                (int) atom color (RBG triplet)
529cs+3                (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
530cs+4                (float) Uiso
531cs+5...cs+11        (6 floats) U11, U22, U33, U12, U13, U23
532ci                  (int) unique atom identifier; matches source atom Id in Atom Records
533==============   ===================================================================================
534
535.. _Powder_table:
536
537.. index::
538   single: Powder data object description
539   single: Data object descriptions; Powder Data
540
541Powder Diffraction Tree Items
542-----------------------------
543
544Every powder diffraction histogram is stored in the GSAS-II data tree
545with a top-level entry named beginning with the string "PWDR ". The
546diffraction data for that information are directly associated with
547that tree item and there are a series of children to that item. The
548routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
549and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
550load this information into a dictionary where the child tree name is
551used as a key, and the information in the main entry is assigned
552a key of ``Data``, as outlined below.
553
554.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
555
556======================     ===============  ===========================================================
557  key                       sub-key          explanation
558======================     ===============  ===========================================================
559Comments                    \               (list of str) Text strings extracted from the original powder
560                                            data header. These cannot be changed by the user;
561                                            it may be empty.
562Limits                      \               (list) two two element lists, as [[Ld,Hd],[L,H]]
563                                            where L and Ld are the current and default lowest
564                                            two-theta value to be used and
565                                            where H and Hd are the current and default highest
566                                            two-theta value to be used.
567Reflection Lists            \               (dict of dicts) with an entry for each phase in the
568                                            histogram. The contents of each dict item
569                                            is a dict containing reflections, as described in
570                                            the :ref:`Powder Reflections <PowderRefl_table>`
571                                            description.
572Instrument Parameters       \               (dict) The instrument parameters uses different dicts
573                                            for the constant wavelength (CW) and time-of-flight (TOF)
574                                            cases. See below for the descriptions of each.
575wtFactor                    \               (float) A weighting factor to increase or decrease
576                                            the leverage of data in the histogram .
577                                            A value of 1.0 weights the data with their
578                                            standard uncertainties and a larger value
579                                            increases the weighting of the data (equivalent
580                                            to decreasing the uncertainties).
581Sample Parameters           \               (dict) Parameters that describe how
582                                            the data were collected, as listed
583                                            below. Refinable parameters are a list containing
584                                            a float and a bool, where the second value
585                                            specifies if the value is refined, otherwise
586                                            the value is a float unless otherwise noted.
587\                           Scale           The histogram scale factor (refinable)
588\                           Absorption      The sample absorption coefficient as
589                                            :math:`\\mu r` where r is the radius
590                                            (refinable). Only valid for Debye-Scherrer geometry.
591\                           SurfaceRoughA   Surface roughness parameter A as defined by
592                                            Surotti, *J. Appl. Cryst*, **5**, 325-331, 1972.
593                                            (refinable - only valid for Bragg-Brentano geometry)
594\                           SurfaceRoughB   Surface roughness parameter B (refinable -
595                                            only valid for Bragg-Brentano geometry)
596\                           DisplaceX,      Sample displacement from goniometer center
597                            DisplaceY       where Y is along the beam direction and
598                                            X is perpendicular. Units are :math:`\\mu m`
599                                            (refinable).
600\                           Phi, Chi,       Goniometer sample setting angles, in degrees.
601                            Omega
602\                           Gonio. radius   Radius of the diffractometer in mm
603\                           InstrName       (str) A name for the instrument, used in preparing
604                                            a CIF .
605\                           Force,          Variables that describe how the measurement
606                            Temperature,    was performed. Not used directly in
607                            Humidity,       any computations.
608                            Pressure,
609                            Voltage
610\                           ranId           (int) The random-number Id for the histogram
611                                            (same value as where top-level key is ranId)
612\                           Type            (str) Type of diffraction data, may be 'Debye-Scherrer'
613                                            or 'Bragg-Brentano' .
614hId                         \               (int) The number assigned to the histogram when
615                                            the project is loaded or edited (can change)
616ranId                       \               (int) A random number id for the histogram
617                                            that does not change
618Background                  \               (list) The background is stored as a list with where
619                                            the first item in the list is list and the second
620                                            item is a dict. The list contains the background
621                                            function and its coefficients; the dict contains
622                                            Debye diffuse terms and background peaks.
623                                            (TODO: this needs to be expanded.)
624Data                        \               (list) The data consist of a list of 6 np.arrays
625                                            containing in order:
626
627                                            0. the x-postions (two-theta in degrees),
628                                            1. the intensity values (Yobs),
629                                            2. the weights for each Yobs value
630                                            3. the computed intensity values (Ycalc)
631                                            4. the background values
632                                            5. Yobs-Ycalc
633======================     ===============  ===========================================================
634
635.. _CWPowder_table:
636
637.. index::
638   single: Powder data CW Instrument Parameters
639
640-----------------------------
641CW Instrument Parameters
642-----------------------------
643
644Instrument Parameters are placed in a list of two dicts,
645where the keys in the first dict are listed below. Note that the dict contents are different for
646constant wavelength (CW) vs. time-of-flight (TOF) histograms.
647The value for each item is a list containing three values: the initial value, the current value
648and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
649cannot be refined. The first and second values are floats unless otherwise noted.
650Items not refined are noted as [*]
651
652.. tabularcolumns:: |l|p{1in}|p{4in}|
653
654========================    ===============  ===========================================================
655  key                       sub-key           explanation
656========================    ===============  ===========================================================
657Instrument Parameters[0]    Type [*]            (str) Histogram type:
658                                                * 'PXC' for constant wavelength x-ray
659                                                * 'PNC' for constant wavelength neutron
660\                           Bank [*]            (int) Data set number in a multidata file (usually 1)
661\                           Lam                 (float) Specifies a wavelength in :math:`\\AA`
662\                           Lam1 [*]            (float) Specifies the primary wavelength in
663                                                :math:`\\AA`, used in place of Lam
664                                                when an :math:`\\alpha_1, \\alpha_2`
665                                                source is used.
666\                           Lam2 [*]            (float) Specifies the secondary wavelength in
667                                                :math:`\\AA`, used with Lam1
668\                           I(L2)/I(L1)         (float) Ratio of Lam2 to Lam1, used with Lam1
669\                           Zero                (float) Two-theta zero correction in *degrees*
670\                           Azimuth [*]         (float) Azimuthal setting angle for data recorded with differing setting angles
671\                           U, V, W             (float) Cagliotti profile coefficients
672                                                for Gaussian instrumental broadening, where the
673                                                FWHM goes as
674                                                :math:`U \\tan^2\\theta + V \\tan\\theta + W`
675\                           X, Y, Z             (float) Cauchy (Lorentzian) instrumental broadening coefficients
676\                           SH/L                (float) Variant of the Finger-Cox-Jephcoat asymmetric
677                                                peak broadening ratio. Note that this is the
678                                                sum of S/L and H/L where S is
679                                                sample height, H is the slit height and
680                                                L is the goniometer diameter.
681\                           Polariz.            (float) Polarization coefficient.
682Instrument Parameters[1]                        (empty dict)
683========================    ===============  ===========================================================
684
685.. _TOFPowder_table:
686
687.. index::
688   single: Powder data TOF Instrument Parameters
689
690-----------------------------
691TOF Instrument Parameters
692-----------------------------
693
694Instrument Parameters are also placed in a list of two dicts,
695where the keys in each dict listed below, but here for
696time-of-flight (TOF) histograms.
697The value for each item is a list containing three values: the initial value, the current value
698and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
699cannot be refined. The first and second values are floats unless otherwise noted.
700Items not refined are noted as [*]
701
702.. tabularcolumns:: |l|p{1.5in}|p{4in}|
703
704========================    ===============  ===========================================================
705  key                        sub-key          explanation
706========================    ===============  ===========================================================
707Instrument Parameters[0]    Type [*]            (str) Histogram type:
708                                                * 'PNT' for time of flight neutron
709\                           Bank                (int) Data set number in a multidata file
710\                           2-theta [*]         (float) Nominal scattering angle for the detector
711\                           fltPath [*]         (float) Total flight path source-sample-detector
712\                           Azimuth [*]         (float) Azimuth angle for detector right hand rotation
713                                                from horizontal away from source
714\                           difC,difA,          (float) Diffractometer constants for conversion of d-spacing to TOF
715                            difB                in microseconds
716\                           Zero                (float) Zero point offset (microseconds)
717\                           alpha               (float) Exponential rise profile coefficients
718\                           beta-0              (float) Exponential decay profile coefficients
719                            beta-1
720                            beta-q
721\                           sig-0               (float) Gaussian profile coefficients
722                            sig-1
723                            sig-2
724                            sig-q   
725\                           X,Y,Z               (float) Lorentzian profile coefficients
726Instrument Parameters[1]    Pdabc               (list of 4 float lists) Originally created for use in gsas as optional tables
727                                                of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation
728                                                from the d-spacing and these tables. The d-true column is apparently unused.
729========================    ===============  ===========================================================
730
731
732.. _PowderRefl_table:
733
734.. index::
735   single: Powder reflection object description
736   single: Data object descriptions; Powder Reflections
737
738Powder Reflection Data Structure
739--------------------------------
740
741For every phase in a histogram, the ``Reflection Lists`` value is a dict
742one element of which is `'RefList'`, which is a np.array containing
743reflections. The columns in that array are documented below.
744
745==========  ====================================================
746  index         explanation
747==========  ====================================================
748 0,1,2          h,k,l (float)
749 3              (int) multiplicity
750 4              (float) d-space, :math:`\\AA`
751 5              (float) pos, two-theta
752 6              (float) sig, Gaussian width
753 7              (float) gam, Lorenzian width
754 8              (float) :math:`F_{obs}^2`
755 9              (float) :math:`F_{calc}^2`
756 10             (float) reflection phase, in degrees
757 11             (float) intensity correction for reflection, this times
758                :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
759 12             (float) Preferred orientation correction
760 13             (float) Transmission (absorption correction)
761 14             (float) Extinction correction
762==========  ====================================================
763
764.. _Xtal_table:
765
766.. index::
767   single: Single Crystal data object description
768   single: Data object descriptions; Single crystal data
769
770Single Crystal Tree Items
771-------------------------
772
773Every single crystal diffraction histogram is stored in the GSAS-II data tree
774with a top-level entry named beginning with the string "HKLF ". The
775diffraction data for that information are directly associated with
776that tree item and there are a series of children to that item. The
777routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
778and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
779load this information into a dictionary where the child tree name is
780used as a key, and the information in the main entry is assigned
781a key of ``Data``, as outlined below.
782
783.. tabularcolumns:: |l|l|p{4in}|
784
785======================  ===============     ====================================================
786  key                      sub-key          explanation
787======================  ===============     ====================================================
788Data                        \               (dict) that contains the
789                                            reflection table,
790                                            as described in the
791                                            :ref:`Single Crystal Reflections
792                                            <XtalRefl_table>`
793                                            description.
794
795Instrument Parameters       \               (list) containing two dicts where the possible
796                                            keys in each dict are listed below. The value
797                                            for most items is a list containing two values:
798                                            the initial value, the current value.
799                                            The first and second
800                                            values are floats unless otherwise noted.
801\                           Lam             (two floats) Specifies a wavelength in :math:`\\AA`
802\                           Type            (two str values) Histogram type :
803                                            * 'SXC' for constant wavelength x-ray
804                                            * 'SNC' for constant wavelength neutron
805                                            * 'SNT' for time of flight neutron
806\                           InstrName       (str) A name for the instrument, used in preparing a CIF
807wtFactor                    \               (float) A weighting factor to increase or decrease
808                                            the leverage of data in the histogram.
809                                            A value of 1.0 weights the data with their
810                                            standard uncertainties and a larger value
811                                            increases the weighting of the data (equivalent
812                                            to decreasing the uncertainties).
813
814hId                         \               (int) The number assigned to the histogram when
815                                            the project is loaded or edited (can change)
816ranId                       \               (int) A random number id for the histogram
817                                            that does not change
818======================  ===============     ====================================================
819
820.. _XtalRefl_table:
821
822.. index::
823   single: Single Crystal reflection object description
824   single: Data object descriptions; Single Crystal Reflections
825
826Single Crystal Reflection Data Structure
827----------------------------------------
828
829For every single crystal a histogram, the ``'Data'`` item contains
830the structure factors as an np.array in item `'RefList'`.
831The columns in that array are documented below.
832
833.. tabularcolumns:: |l|p{4in}|
834
835==========  ====================================================
836  index         explanation
837==========  ====================================================
838 0,1,2          (float) h,k,l
839 3              (int) multiplicity
840 4              (float) d-space, :math:`\\AA`
841 5              (float) :math:`F_{obs}^2`
842 6              (float) :math:`\sigma(F_{obs}^2)`
843 7              (float) :math:`F_{calc}^2`
844 8              (float) :math:`F_{obs}^2T`
845 9              (float) :math:`F_{calc}^2T`
846 10             (float) reflection phase, in degrees
847 11             (float) intensity correction for reflection, this times
848                :math:`F_{obs}^2` or :math:`F_{calc}^2`
849                gives Iobs or Icalc
850==========  ====================================================
851
852.. _Image_table:
853
854.. index::
855   image: Image data object description
856   image: Image object descriptions
857
858Image Data Structure
859--------------------
860
861Every 2-dimensional image is stored in the GSAS-II data tree
862with a top-level entry named beginning with the string "IMG ". The
863image data are directly associated with that tree item and there
864are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
865and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
866load this information into a dictionary where the child tree name is
867used as a key, and the information in the main entry is assigned
868a key of ``Data``, as outlined below.
869
870.. tabularcolumns:: |l|l|p{4in}|
871
872======================  ======================  ====================================================
873  key                      sub-key              explanation
874======================  ======================  ====================================================
875Comments                    \                   (list of str) Text strings extracted from the original image data
876                                                header or a metafile. These cannot be changed by
877                                                the user; it may be empty.
878Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
879                                                value. Accomodates
880                                                detector orientations other than with the detector
881                                                X-axis
882                                                horizontal.
883\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
884                                                during image integration multiplied by value. It must have the same size/shape as
885                                                the integrated image. NB: value < 0 for subtraction.
886\                           calibrant           (str) The material used for determining the position/orientation
887                                                of the image. The data is obtained from :func:`ImageCalibrants`
888                                                and UserCalibrants.py (supplied by user).
889\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
890\                           calibskip           (int) The number of expected diffraction lines skipped during the last
891                                                calibration run.
892\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
893                                                strikes the detector plane as determined by calibration. This point
894                                                does not have to be within the limits of the detector boundaries.
895\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
896                                                of the image is at the center line otherwise it is at the leading edge.
897\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
898\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
899                                                calibration calculations. See pixLimit for details as how point is found.
900\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
901                                                ring offset at higher angles. Optionally determined by calibration.
902\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
903\                           distance            (float) The distance (mm) from sample to detector plane.
904\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
905                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
906                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
907                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
908                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
909\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
910\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
911\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
912                                                Required for texture calculations.
913\                           invert_x            (bool) If True display the image with the x-axis inverted.
914\                           invert_y            (bool) If True display the image with the y-axis inverted.
915\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
916\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
917\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
918                                                intensities obtained during integration.
919\                           outAzimuths         (int) The number of azimuth pie slices.
920\                           outChannels         (int) The number of 2-theta steps.
921\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
922\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
923                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
924                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
925                                                Locations are used to construct rings of points for calibration calcualtions.
926\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
927                                                integration using value.
928\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
929                                                diffraction ring with the same d-spacing (dsp)
930\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
931                                                selected by the user,
932\                           Range               (list) The minimum & maximum values of the image
933\                           rotation            (float) The angle between the x-axis and the vector about which the
934                                                detector is tilted. Constrained to -180 to 180 deg.
935\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
936                                                calculations.
937\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
938                                                to cause correction to be applied.
939\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
940\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
941\                           showLines           (bool) If True then isplay the integration limits to be used.
942\                           size                (list:int) The number of pixels on the image x & y axes
943\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
944\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
945\                           wavelength          (float) The radiation wavelength (:math:`\\AA`) as entered by the user
946                                                (or someday obtained from the image header).
947Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
948                                                to be excluded from integration
949\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
950                                                of which is excluded from recalibration and integration. Only one frame is allowed.
951\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
952                                                from integration.
953\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
954                                                to be excluded from integration.
955\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
956                                                to be excluded from integration.
957\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
958                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
959\                           SpotMask            (dict: int & array)
960                                                'esdMul'(int) number of standard deviations above mean ring intensity to mask
961                                                'spotMask' (bool array) the spot mask for every pixel in image         
962
963Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
964\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
965                                                These will be restricted by space group symmetry; result of strain fit refinement.
966\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
967\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
968                                                and are used to determine the strain tensor.
969                                                The dictionary items are:
970                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
971                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
972                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
973                                                'Esig': (list: float) Esds for Emat from fitting.
974                                                'pixLimit': (int) Search range to find highest point on ring for each data point
975                                                'cutoff': (float) I/Ib cutoff for searching.
976                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
977                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
978                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
979
980======================  ======================  ====================================================
981
982.. _parmDict_table:
983
984.. index::
985   single: Parameter dictionary
986
987Parameter Dictionary
988-------------------------
989
990The parameter dictionary contains all of the variable parameters for the refinement.
991The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
992It is prepared in two ways. When loaded from the tree
993(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
994:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
995the values are lists with two elements: ``[value, refine flag]``
996
997When loaded from the GPX file (in
998:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
999dict is the actual parameter value (usually a float, but sometimes a
1000letter or string flag value (such as I or A for iso/anisotropic).
1001
1002ISODISTORT implementation
1003------------------------------
1004
1005CIFs prepared with the ISODISTORT web site
1006https://stokes.byu.edu/iso/isodistort_version5.6.1/isodistort.php
1007[B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions." J. Appl. Cryst. 39, 607-614 (2006).]
1008can be read into GSAS-II using import CIF. This will cause constraints to be established for structural distortion modes read from the CIF.
1009At present, of the five types of modes  only displacive(``_iso_displacivemode``...) and occupancy (``_iso_occupancymode``...) are processed. Not yet processed: ``_iso_magneticmode``..., ``_iso_rotationalmode``... & ``_iso_strainmode``...
1010
1011The CIF importer :mod:`G2phase_CIF` implements class :class:`G2phase_CIF.CIFPhaseReader` which offers two methods associated with ISODISTORT (ID) input. Method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_test`
1012checks to see if a CIF block contains the loops with ``_iso_displacivemode_label`` or  ``_iso_occupancymode_label`` items.
1013If so, method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_proc` is called to read and interpret them.
1014The results are placed into the reader object's ``.Phase`` class variable as a dict item with key ``'ISODISTORT'``.
1015
1016Note that each mode ID has a long label with a name such as  Pm-3m[1/2,1/2,1/2]R5+(a,a,0)[La:b:dsp]T1u(a). Function :func:`G2phase_CIF.ISODISTORT_shortLbl` is used to create a short name for this,
1017such as R5_T1u(a) which is made unique by addition of _n if the short name is duplicated.
1018As each mode is processed, a constraint corresponding to that mode is
1019created and is added to list in the reader object's ``.Constraints`` class variable. Items placed into that list can either be a list, which corresponds to a function (new var) type :ref:`constraint definition <Constraints_table>` entry, or an item can be a dict, which provides help information for each constraint.
1020
1021------------------------------
1022Displacive modes
1023------------------------------
1024
1025The coordinate variables, as named by ISODISTORT, are placed in
1026``.Phase['ISODISTORT']['IsoVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2VarList']``. The mode variables,
1027as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2ModeList']``.
1028[Use ``str(G2VarObj)`` to get the variable name from the G2VarObj object, but note that the phase number, *n*, for the prefix "*n*::" cannot be determined as the phase number is not yet assigned.]
1029
1030Displacive modes are a bit complex in that they relate to delta displacements, relative to an offset value for each coordinate, and because the modes are normalized, while GSAS-II also uses displacements, but these are added to the coordinates after each refinement cycle and the delta values are set to zero. ISODISTORT uses fixed offsets (subtracted from the actual position to obtain the delta values) that are taken from ``_iso_coordinate_formula`` and these are placed in ``.Phase['ISODISTORT']['ParentStructure]`` (keyed by atom label). The normalization factors (which the delta values are divided by) are taken from ``_iso_displacivemodenorm_value`` and are placed in ``.Phase['ISODISTORT']['NormList']`` in the same order as as ``...['IsoModeList']`` and
1031``...['G2ModeList']``.
1032
1033The CIF contains a sparse matrix, from the ``loop_`` containing
1034``_iso_displacivemodematrix_value`` which provides the equations for determining the mode values from the coordinates, that matrix is placed in ``.Phase['ISODISTORT']['Mode2VarMatrix']``. The matrix is inverted to produce
1035``.Phase['ISODISTORT']['Var2ModeMatrix']``, which determines how to compute the
1036mode values from the delta coordinate values. These values are used for the
1037in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1038values, the latter with s.u. values.
1039
1040
1041------------------------------
1042Occupancy modes
1043------------------------------
1044
1045
1046The delta occupancy variables, as named by ISODISTORT, are placed in
1047``.Phase['ISODISTORT']['OccVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2OccVarList']``. The mode variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['OccModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2OccModeList']``.
1048
1049Occupancy modes, like Displacive modes, are also refined as delta values.  However, GSAS-II directly refines the fractional occupancies.
1050Offset values for each atom, are taken from ``_iso_occupancy_formula`` and are placed in
1051``.Phase['ISODISTORT']['ParentOcc]``.
1052(Offset values are subtracted from the actual position to obtain the delta values.)
1053Modes are normalized (where the mode values are divided by the normalization factor)
1054are taken from ``_iso_occupancymodenorm_value`` and are placed in ``.Phase['ISODISTORT']['OccNormList']`` in the same order as as ``...['OccModeList']`` and
1055``...['G2OccModeList']``.
1056
1057The CIF contains a sparse matrix, from the ``loop_`` containing
1058``_iso_occupancymodematrix_value``, which provides the equations for determining the mode values from the coordinates. That matrix is placed in ``.Phase['ISODISTORT']['Occ2VarMatrix']``. The matrix is inverted to produce
1059``.Phase['ISODISTORT']['Var2OccMatrix']``, which determines how to compute the
1060mode values from the delta coordinate values.
1061
1062
1063------------------------------
1064Mode Computations
1065------------------------------
1066
1067Constraints are processed after the CIF has been read in
1068:meth:`GSASIIdataGUI.GSASII.OnImportPhase` or 
1069:meth:`GSASIIscriptable.G2Project.add_phase` by moving them from the reader
1070object's ``.Constraints`` class variable to
1071the Constraints tree entry's ['Phase'] list (for list items defining constraints) or
1072the Constraints tree entry's ['_Explain'] dict (for dict items defining constraint help information)
1073
1074The information in ``.Phase['ISODISTORT']`` is used
1075in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1076values, the latter with s.u. values. This can be called from the Constraints and Phase/Atoms tree items.
1077
1078Before each refinement, constraints are processed as
1079:ref:`described elsewhere <Constraints_processing>`. After a refinement
1080is complete, :func:`GSASIImapvars.PrintIndependentVars` shows the
1081shifts and s.u.'s on the refined modes, using GSAS-II values, but
1082:func:`GSASIIstrIO.PrintISOmodes` prints the ISODISTORT modes as computed
1083in the web site.
1084
1085
1086*Classes and routines*
1087----------------------
1088
1089'''
1090from __future__ import division, print_function
1091import platform
1092import re
1093import imp
1094import random as ran
1095import sys
1096import os.path as ospath
1097if '2' in platform.python_version_tuple()[0]:
1098    import cPickle
1099else:
1100    import pickle as cPickle
1101import GSASIIpath
1102import GSASIImath as G2mth
1103import GSASIIspc as G2spc
1104import numpy as np
1105
1106GSASIIpath.SetVersionNumber("$Revision: 4399 $")
1107
1108DefaultControls = {
1109    'deriv type':'analytic Hessian',
1110    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
1111    'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
1112    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
1113    'Author':'no name',
1114    'FreePrm1':'Sample humidity (%)',
1115    'FreePrm2':'Sample voltage (V)',
1116    'FreePrm3':'Applied load (MN)',
1117    'ShowCell':False,
1118    }
1119'''Values to be used as defaults for the initial contents of the ``Controls``
1120data tree item.
1121'''
1122def StripUnicode(string,subs='.'):
1123    '''Strip non-ASCII characters from strings
1124
1125    :param str string: string to strip Unicode characters from
1126    :param str subs: character(s) to place into string in place of each
1127      Unicode character. Defaults to '.'
1128
1129    :returns: a new string with only ASCII characters
1130    '''
1131    s = ''
1132    for c in string:
1133        if ord(c) < 128:
1134            s += c
1135        else:
1136            s += subs
1137    return s
1138#    return s.encode('ascii','replace')
1139
1140def MakeUniqueLabel(lbl,labellist):
1141    '''Make sure that every a label is unique against a list by adding
1142    digits at the end until it is not found in list.
1143
1144    :param str lbl: the input label
1145    :param list labellist: the labels that have already been encountered
1146    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
1147      ``_10-99``, etc.) appended at the end
1148    '''
1149    lbl = StripUnicode(lbl.strip(),'_')
1150    if not lbl: # deal with a blank label
1151        lbl = '_1'
1152    if lbl not in labellist:
1153        labellist.append(lbl)
1154        return lbl
1155    i = 1
1156    prefix = lbl
1157    if '_' in lbl:
1158        prefix = lbl[:lbl.rfind('_')]
1159        suffix = lbl[lbl.rfind('_')+1:]
1160        try:
1161            i = int(suffix)+1
1162        except: # suffix could not be parsed
1163            i = 1
1164            prefix = lbl
1165    while prefix+'_'+str(i) in labellist:
1166        i += 1
1167    else:
1168        lbl = prefix+'_'+str(i)
1169        labellist.append(lbl)
1170    return lbl
1171
1172PhaseIdLookup = {}
1173'''dict listing phase name and random Id keyed by sequential phase index as a str;
1174best to access this using :func:`LookupPhaseName`
1175'''
1176PhaseRanIdLookup = {}
1177'''dict listing phase sequential index keyed by phase random Id;
1178best to access this using :func:`LookupPhaseId`
1179'''
1180HistIdLookup = {}
1181'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
1182best to access this using :func:`LookupHistName`
1183'''
1184HistRanIdLookup = {}
1185'''dict listing histogram sequential index keyed by histogram random Id;
1186best to access this using :func:`LookupHistId`
1187'''
1188AtomIdLookup = {}
1189'''dict listing for each phase index as a str, the atom label and atom random Id,
1190keyed by atom sequential index as a str;
1191best to access this using :func:`LookupAtomLabel`
1192'''
1193AtomRanIdLookup = {}
1194'''dict listing for each phase the atom sequential index keyed by atom random Id;
1195best to access this using :func:`LookupAtomId`
1196'''
1197ShortPhaseNames = {}
1198'''a dict containing a possibly shortened and when non-unique numbered
1199version of the phase name. Keyed by the phase sequential index.
1200'''
1201ShortHistNames = {}
1202'''a dict containing a possibly shortened and when non-unique numbered
1203version of the histogram name. Keyed by the histogram sequential index.
1204'''
1205
1206#VarDesc = {}  # removed 1/30/19 BHT as no longer needed (I think)
1207#''' This dictionary lists descriptions for GSAS-II variables,
1208#as set in :func:`CompileVarDesc`. See that function for a description
1209#for how keys and values are written.
1210#'''
1211
1212reVarDesc = {}
1213''' This dictionary lists descriptions for GSAS-II variables where
1214keys are compiled regular expressions that will match the name portion
1215of a parameter name. Initialized in :func:`CompileVarDesc`.
1216'''
1217
1218reVarStep = {}
1219''' This dictionary lists the preferred step size for numerical
1220derivative computation w/r to a GSAS-II variable. Keys are compiled
1221regular expressions and values are the step size for that parameter.
1222Initialized in :func:`CompileVarDesc`.
1223'''
1224# create a default space group object for P1; N.B. fails when building documentation
1225try:
1226    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1227except:
1228    pass
1229
1230def GetPhaseNames(fl):
1231    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1232    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1233
1234    :param file fl: opened .gpx file
1235    :return: list of phase names
1236    '''
1237    PhaseNames = []
1238    while True:
1239        try:
1240            data = cPickle.load(fl)
1241        except EOFError:
1242            break
1243        datum = data[0]
1244        if 'Phases' == datum[0]:
1245            for datus in data[1:]:
1246                PhaseNames.append(datus[0])
1247    fl.seek(0)          #reposition file
1248    return PhaseNames
1249
1250def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1251    '''Create a new phase dict with default values for various parameters
1252
1253    :param str Name: Name for new Phase
1254
1255    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1256      defaults to data for P 1
1257
1258    :param list cell: unit cell parameter list; defaults to
1259      [1.0,1.0,1.0,90.,90,90.,1.]
1260
1261    '''
1262    if SGData is None: SGData = P1SGData
1263    if cell is None: cell=[1.0,1.0,1.0,90.,90.,90.,1.]
1264    phaseData = {
1265        'ranId':ran.randint(0,sys.maxsize),
1266        'General':{
1267            'Name':Name,
1268            'Type':'nuclear',
1269            'Modulated':False,
1270            'AtomPtrs':[3,1,7,9],
1271            'SGData':SGData,
1272            'Cell':[False,]+cell,
1273            'Pawley dmin':1.0,
1274            'Data plot type':'None',
1275            'SH Texture':{
1276                'Order':0,
1277                'Model':'cylindrical',
1278                'Sample omega':[False,0.0],
1279                'Sample chi':[False,0.0],
1280                'Sample phi':[False,0.0],
1281                'SH Coeff':[False,{}],
1282                'SHShow':False,
1283                'PFhkl':[0,0,1],
1284                'PFxyz':[0,0,1],
1285                'PlotType':'Pole figure',
1286                'Penalty':[['',],0.1,False,1.0]}},
1287        'Atoms':[],
1288        'Drawing':{},
1289        'Histograms':{},
1290        'Pawley ref':[],
1291        'RBModels':{},
1292        }
1293    if Super and Super.get('Use',False):
1294        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1295        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])[1]
1296        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1297
1298    return phaseData
1299
1300def ReadCIF(URLorFile):
1301    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1302    (from James Hester).
1303    The open routine gets confused with DOS names that begin with a letter and colon
1304    "C:\dir\" so this routine will try to open the passed name as a file and if that
1305    fails, try it as a URL
1306
1307    :param str URLorFile: string containing a URL or a file name. Code will try first
1308      to open it as a file and then as a URL.
1309
1310    :returns: a PyCifRW CIF object.
1311    '''
1312    import CifFile as cif # PyCifRW from James Hester
1313
1314    # alternate approach:
1315    #import urllib
1316    #ciffile = 'file:'+urllib.pathname2url(filename)
1317
1318    try:
1319        fp = open(URLorFile,'r')
1320        cf = cif.ReadCif(fp)
1321        fp.close()
1322        return cf
1323    except IOError:
1324        return cif.ReadCif(URLorFile)
1325
1326def IndexAllIds(Histograms,Phases):
1327    '''Scan through the used phases & histograms and create an index
1328    to the random numbers of phases, histograms and atoms. While doing this,
1329    confirm that assigned random numbers are unique -- just in case lightning
1330    strikes twice in the same place.
1331
1332    Note: this code assumes that the atom random Id (ranId) is the last
1333    element each atom record.
1334
1335    This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
1336    (which loads the histograms and phases from a GPX file),
1337    :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
1338    (which loads the histograms and phases from the data tree.) and
1339    :meth:`GSASIIconstrGUI.UpdateConstraints`
1340    (which displays & edits the constraints in a GUI)
1341
1342    TODO: do we need a lookup for rigid body variables?
1343    '''
1344    # process phases and atoms
1345    PhaseIdLookup.clear()
1346    PhaseRanIdLookup.clear()
1347    AtomIdLookup.clear()
1348    AtomRanIdLookup.clear()
1349    ShortPhaseNames.clear()
1350    for ph in Phases:
1351        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1352        ranId = Phases[ph]['ranId']
1353        while ranId in PhaseRanIdLookup:
1354            # Found duplicate random Id! note and reassign
1355            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1356            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1357        pId = str(Phases[ph]['pId'])
1358        PhaseIdLookup[pId] = (ph,ranId)
1359        PhaseRanIdLookup[ranId] = pId
1360        shortname = ph  #[:10]
1361        while shortname in ShortPhaseNames.values():
1362            shortname = ph[:8] + ' ('+ pId + ')'
1363        ShortPhaseNames[pId] = shortname
1364        AtomIdLookup[pId] = {}
1365        AtomRanIdLookup[pId] = {}
1366        for iatm,at in enumerate(Phases[ph]['Atoms']):
1367            ranId = at[cia+8]
1368            while ranId in AtomRanIdLookup[pId]: # check for dups
1369                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1370                at[cia+8] = ranId = ran.randint(0,sys.maxsize)
1371            AtomRanIdLookup[pId][ranId] = str(iatm)
1372            if Phases[ph]['General']['Type'] == 'macromolecular':
1373                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1374            else:
1375                label = at[ct-1]
1376            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1377    # process histograms
1378    HistIdLookup.clear()
1379    HistRanIdLookup.clear()
1380    ShortHistNames.clear()
1381    for hist in Histograms:
1382        ranId = Histograms[hist]['ranId']
1383        while ranId in HistRanIdLookup:
1384            # Found duplicate random Id! note and reassign
1385            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1386            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1387        hId = str(Histograms[hist]['hId'])
1388        HistIdLookup[hId] = (hist,ranId)
1389        HistRanIdLookup[ranId] = hId
1390        shortname = hist[:15]
1391        while shortname in ShortHistNames.values():
1392            shortname = hist[:11] + ' ('+ hId + ')'
1393        ShortHistNames[hId] = shortname
1394
1395def LookupAtomId(pId,ranId):
1396    '''Get the atom number from a phase and atom random Id
1397
1398    :param int/str pId: the sequential number of the phase
1399    :param int ranId: the random Id assigned to an atom
1400
1401    :returns: the index number of the atom (str)
1402    '''
1403    if not AtomRanIdLookup:
1404        raise Exception('Error: LookupAtomId called before IndexAllIds was run')
1405    if pId is None or pId == '':
1406        raise KeyError('Error: phase is invalid (None or blank)')
1407    pId = str(pId)
1408    if pId not in AtomRanIdLookup:
1409        raise KeyError('Error: LookupAtomId does not have phase '+pId)
1410    if ranId not in AtomRanIdLookup[pId]:
1411        raise KeyError('Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']')
1412    return AtomRanIdLookup[pId][ranId]
1413
1414def LookupAtomLabel(pId,index):
1415    '''Get the atom label from a phase and atom index number
1416
1417    :param int/str pId: the sequential number of the phase
1418    :param int index: the index of the atom in the list of atoms
1419
1420    :returns: the label for the atom (str) and the random Id of the atom (int)
1421    '''
1422    if not AtomIdLookup:
1423        raise Exception('Error: LookupAtomLabel called before IndexAllIds was run')
1424    if pId is None or pId == '':
1425        raise KeyError('Error: phase is invalid (None or blank)')
1426    pId = str(pId)
1427    if pId not in AtomIdLookup:
1428        raise KeyError('Error: LookupAtomLabel does not have phase '+pId)
1429    if index not in AtomIdLookup[pId]:
1430        raise KeyError('Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']')
1431    return AtomIdLookup[pId][index]
1432
1433def LookupPhaseId(ranId):
1434    '''Get the phase number and name from a phase random Id
1435
1436    :param int ranId: the random Id assigned to a phase
1437    :returns: the sequential Id (pId) number for the phase (str)
1438    '''
1439    if not PhaseRanIdLookup:
1440        raise Exception('Error: LookupPhaseId called before IndexAllIds was run')
1441    if ranId not in PhaseRanIdLookup:
1442        raise KeyError('Error: LookupPhaseId does not have ranId '+str(ranId))
1443    return PhaseRanIdLookup[ranId]
1444
1445def LookupPhaseName(pId):
1446    '''Get the phase number and name from a phase Id
1447
1448    :param int/str pId: the sequential assigned to a phase
1449    :returns:  (phase,ranId) where phase is the name of the phase (str)
1450      and ranId is the random # id for the phase (int)
1451    '''
1452    if not PhaseIdLookup:
1453        raise Exception('Error: LookupPhaseName called before IndexAllIds was run')
1454    if pId is None or pId == '':
1455        raise KeyError('Error: phase is invalid (None or blank)')
1456    pId = str(pId)
1457    if pId not in PhaseIdLookup:
1458        raise KeyError('Error: LookupPhaseName does not have index '+pId)
1459    return PhaseIdLookup[pId]
1460
1461def LookupHistId(ranId):
1462    '''Get the histogram number and name from a histogram random Id
1463
1464    :param int ranId: the random Id assigned to a histogram
1465    :returns: the sequential Id (hId) number for the histogram (str)
1466    '''
1467    if not HistRanIdLookup:
1468        raise Exception('Error: LookupHistId called before IndexAllIds was run')
1469    if ranId not in HistRanIdLookup:
1470        raise KeyError('Error: LookupHistId does not have ranId '+str(ranId))
1471    return HistRanIdLookup[ranId]
1472
1473def LookupHistName(hId):
1474    '''Get the histogram number and name from a histogram Id
1475
1476    :param int/str hId: the sequential assigned to a histogram
1477    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1478      and ranId is the random # id for the histogram (int)
1479    '''
1480    if not HistIdLookup:
1481        raise Exception('Error: LookupHistName called before IndexAllIds was run')
1482    if hId is None or hId == '':
1483        raise KeyError('Error: histogram is invalid (None or blank)')
1484    hId = str(hId)
1485    if hId not in HistIdLookup:
1486        raise KeyError('Error: LookupHistName does not have index '+hId)
1487    return HistIdLookup[hId]
1488
1489def fmtVarDescr(varname):
1490    '''Return a string with a more complete description for a GSAS-II variable
1491
1492    :param str varname: A full G2 variable name with 2 or 3 or 4
1493       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1494
1495    :returns: a string with the description
1496    '''
1497    s,l = VarDescr(varname)
1498    return s+": "+l
1499
1500def VarDescr(varname):
1501    '''Return two strings with a more complete description for a GSAS-II variable
1502
1503    :param str name: A full G2 variable name with 2 or 3 or 4
1504       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1505
1506    :returns: (loc,meaning) where loc describes what item the variable is mapped
1507      (phase, histogram, etc.) and meaning describes what the variable does.
1508    '''
1509
1510    # special handling for parameter names without a colon
1511    # for now, assume self-defining
1512    if varname.find(':') == -1:
1513        return "Global",varname
1514
1515    l = getVarDescr(varname)
1516    if not l:
1517        return ("invalid variable name ("+str(varname)+")!"),""
1518#        return "invalid variable name!",""
1519
1520    if not l[-1]:
1521        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1522
1523    if len(l) == 3:         #SASD variable name!
1524        s = 'component:'+l[1]
1525        return s,l[-1]
1526    s = ""
1527    if l[0] is not None and l[1] is not None: # HAP: keep short
1528        if l[2] == "Scale": # fix up ambigous name
1529            l[5] = "Phase fraction"
1530        if l[0] == '*':
1531            lbl = 'Seq. ref.'
1532        else:
1533            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1534        if l[1] == '*':
1535            hlbl = 'Seq. ref.'
1536        else:
1537            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1538        if hlbl[:4] == 'HKLF':
1539            hlbl = 'Xtl='+hlbl[5:]
1540        elif hlbl[:4] == 'PWDR':
1541            hlbl = 'Pwd='+hlbl[5:]
1542        else:
1543            hlbl = 'Hist='+hlbl
1544        s = "Ph="+str(lbl)+" * "+str(hlbl)
1545    else:
1546        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1547            l[5] = "Scale factor"
1548        if l[2] == 'Back': # background parameters are "special", alas
1549            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1550            l[-1] += ' #'+str(l[3])
1551        elif l[4] is not None: # rigid body parameter or modulation parm
1552            lbl = ShortPhaseNames.get(l[0],'phase?')
1553            if 'RB' in l[2]:    #rigid body parm
1554                s = "Res #"+str(l[3])+" body #"+str(l[4])+" in "+str(lbl)
1555            else: #modulation parm
1556                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1557        elif l[3] is not None: # atom parameter,
1558            lbl = ShortPhaseNames.get(l[0],'phase?')
1559            try:
1560                albl = LookupAtomLabel(l[0],l[3])[0]
1561            except KeyError:
1562                albl = 'Atom?'
1563            s = "Atom "+str(albl)+" in "+str(lbl)
1564        elif l[0] == '*':
1565            s = "All phases "
1566        elif l[0] is not None:
1567            lbl = ShortPhaseNames.get(l[0],'phase?')
1568            s = "Phase "+str(lbl)
1569        elif l[1] == '*':
1570            s = 'All hists'
1571        elif l[1] is not None:
1572            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1573            if hlbl[:4] == 'HKLF':
1574                hlbl = 'Xtl='+hlbl[5:]
1575            elif hlbl[:4] == 'PWDR':
1576                hlbl = 'Pwd='+hlbl[5:]
1577            else:
1578                hlbl = 'Hist='+hlbl
1579            s = str(hlbl)
1580    if not s:
1581        s = 'Global'
1582    return s,l[-1]
1583
1584def getVarDescr(varname):
1585    '''Return a short description for a GSAS-II variable
1586
1587    :param str name: A full G2 variable name with 2 or 3 or 4
1588       colons (<p>:<h>:name[:<a1>][:<a2>])
1589
1590    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1591      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1592      the histogram number and the atom number; `name` will always be
1593      a str; and `description` is str or `None`.
1594      If the variable name is incorrectly formed (for example, wrong
1595      number of colons), `None` is returned instead of a list.
1596    '''
1597    l = varname.split(':')
1598    if len(l) == 2:     #SASD parameter name
1599        return varname,l[0],getDescr(l[1])
1600    if len(l) == 3:
1601        l += [None,None]
1602    elif len(l) == 4:
1603        l += [None]
1604    elif len(l) != 5:
1605        return None
1606    for i in (0,1,3,4):
1607        if l[i] == "":
1608            l[i] = None
1609    l += [getDescr(l[2])]
1610    return l
1611
1612def CompileVarDesc():
1613    '''Set the values in the variable lookup tables
1614    (:attr:`reVarDesc` and :attr:`reVarStep`).
1615    This is called in :func:`getDescr` and :func:`getVarStep` so this
1616    initialization is always done before use.
1617
1618    Note that keys may contain regular expressions, where '[xyz]'
1619    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range
1620    of values). '.*' matches any string. For example::
1621
1622    'AUiso':'Atomic isotropic displacement parameter',
1623
1624    will match variable ``'p::AUiso:a'``.
1625    If parentheses are used in the key, the contents of those parentheses can be
1626    used in the value, such as::
1627
1628    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1629
1630    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1631    in the value when used.
1632
1633    '''
1634    if reVarDesc: return # already done
1635    for key,value in {
1636        # derived or other sequential vars
1637        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1638        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1639        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1640        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1641        # ambiguous, alas:
1642        'Scale' : 'Phase or Histogram scale factor',
1643        # Phase vars (p::<var>)
1644        'A([0-5])' : ('Reciprocal metric tensor component \\1',1e-5),
1645        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1646        # Atom vars (p::<var>:a)
1647        'dA([xyz])$' : ('change to atomic coordinate, \\1',1e-6),
1648        'A([xyz])$' : '\\1 fractional atomic coordinate',
1649        'AUiso':('Atomic isotropic displacement parameter',1e-4),
1650        'AU([123][123])':('Atomic anisotropic displacement parameter U\\1',1e-4),
1651        'Afrac': ('Atomic site fraction parameter',1e-5),
1652        'Amul': 'Atomic site multiplicity value',
1653        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1654        # Hist & Phase (HAP) vars (p:h:<var>)
1655        'Back': 'Background term',
1656        'BkPkint;(.*)':'Background peak #\\1 intensity',
1657        'BkPkpos;(.*)':'Background peak #\\1 position',
1658        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1659        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1660        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1661        'D([123][123])' : 'Anisotropic strain coef. \\1',
1662        'Extinction' : 'Extinction coef.',
1663        'MD' : 'March-Dollase coef.',
1664        'Mustrain;.*' : 'Microstrain coef.',
1665        'Size;.*' : 'Crystallite size value',
1666        'eA$' : 'Cubic mustrain value',
1667        'Ep$' : 'Primary extinction',
1668        'Es$' : 'Secondary type II extinction',
1669        'Eg$' : 'Secondary type I extinction',
1670        'Flack' : 'Flack parameter',
1671        'TwinFr' : 'Twin fraction',
1672        'Layer Disp'  : 'Layer displacement along beam',
1673        #Histogram vars (:h:<var>)
1674        'Absorption' : 'Absorption coef.',
1675        'Displace([XY])' : ('Debye-Scherrer sample displacement \\1',0.1),
1676        'Lam' : ('Wavelength',1e-6),
1677        'I\(L2\)\/I\(L1\)' : ('Ka2/Ka1 intensity ratio',0.001),
1678        'Polariz\.' : ('Polarization correction',1e-3),
1679        'SH/L' : ('FCJ peak asymmetry correction',1e-4),
1680        '([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),
1681        '([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),
1682        'Zero' : 'Debye-Scherrer zero correction',
1683        'Shift' : 'Bragg-Brentano sample displ.',
1684        'SurfRoughA' : 'Bragg-Brenano surface roughness A',
1685        'SurfRoughB' : 'Bragg-Brenano surface roughness B',
1686        'Transparency' : 'Bragg-Brentano sample tranparency',
1687        'DebyeA' : 'Debye model amplitude',
1688        'DebyeR' : 'Debye model radius',
1689        'DebyeU' : 'Debye model Uiso',
1690        'RBV.*' : 'Vector rigid body parameter',
1691        'RBR.*' : 'Residue rigid body parameter',
1692        'RBRO([aijk])' : 'Residue rigid body orientation parameter',
1693        'RBRP([xyz])' : 'Residue rigid body position parameter',
1694        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1695        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1696        'constr([0-9]*)' : 'Parameter from constraint',
1697        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1698        'mV([0-2])$' : 'Modulation vector component \\1',
1699        'Fsin'  :   'Sin site fraction modulation',
1700        'Fcos'  :   'Cos site fraction modulation',
1701        'Fzero'  :   'Crenel function offset',      #may go away
1702        'Fwid'   :   'Crenel function width',
1703        'Tmin'   :   'ZigZag/Block min location',
1704        'Tmax'   :   'ZigZag/Block max location',
1705        '([XYZ])max': 'ZigZag/Block max value for \\1',
1706        '([XYZ])sin'  : 'Sin position wave for \\1',
1707        '([XYZ])cos'  : 'Cos position wave for \\1',
1708        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1709        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1710        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1711        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1712        # PDF peak parms (l:<var>;l = peak no.)
1713        'PDFpos'  : 'PDF peak position',
1714        'PDFmag'  : 'PDF peak magnitude',
1715        'PDFsig'  : 'PDF peak std. dev.',
1716        # SASD vars (l:<var>;l = component)
1717        'Aspect ratio' : 'Particle aspect ratio',
1718        'Length' : 'Cylinder length',
1719        'Diameter' : 'Cylinder/disk diameter',
1720        'Thickness' : 'Disk thickness',
1721        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1722        'Dist' : 'Interparticle distance',
1723        'VolFr' : 'Dense scatterer volume fraction',
1724        'epis' : 'Sticky sphere epsilon',
1725        'Sticky' : 'Stickyness',
1726        'Depth' : 'Well depth',
1727        'Width' : 'Well width',
1728        'Volume' : 'Particle volume',
1729        'Radius' : 'Sphere/cylinder/disk radius',
1730        'Mean' : 'Particle mean radius',
1731        'StdDev' : 'Standard deviation in Mean',
1732        'G$': 'Guinier prefactor',
1733        'Rg$': 'Guinier radius of gyration',
1734        'B$': 'Porod prefactor',
1735        'P$': 'Porod power',
1736        'Cutoff': 'Porod cutoff',
1737        'PkInt': 'Bragg peak intensity',
1738        'PkPos': 'Bragg peak position',
1739        'PkSig': 'Bragg peak sigma',
1740        'PkGam': 'Bragg peak gamma',
1741        'e([12][12])' : 'strain tensor e\1',   # strain vars e11, e22, e12
1742        'Dcalc': 'Calc. d-spacing',
1743        'Back$': 'background parameter',
1744        'pos$': 'peak position',
1745        'int$': 'peak intensity',
1746        'WgtFrac':'phase weight fraction',
1747        'alpha':'TOF profile term',
1748        'beta-[01q]':'TOF profile term',
1749        'sig-[012q]':'TOF profile term',
1750        'dif[ABC]':'TOF to d-space calibration',
1751        'C\([0-9]*,[0-9]*\)' : 'spherical harmonics preferred orientation coef.',
1752        }.items():
1753        if len(value) == 2:
1754            #VarDesc[key] = value[0]
1755            reVarDesc[re.compile(key)] = value[0]
1756            reVarStep[re.compile(key)] = value[1]
1757        else:
1758            #VarDesc[key] = value
1759            reVarDesc[re.compile(key)] = value
1760
1761def removeNonRefined(parmList):
1762    '''Remove items from variable list that are not refined and should not
1763    appear as options for constraints
1764
1765    :param list parmList: a list of strings of form "p:h:VAR:a" where
1766      VAR is the variable name
1767
1768    :returns: a list after removing variables where VAR matches a
1769      entry in local variable NonRefinedList
1770    '''
1771    NonRefinedList = ['Omega','Type','Chi','Phi', 'Azimuth','Gonio. radius',
1772                          'Lam1','Lam2','Back','Temperature','Pressure',
1773                          'FreePrm1','FreePrm2','FreePrm3',
1774                          'Source','nPeaks','LeBail','newLeBail','Bank',
1775                          'nDebye', #'',
1776                    ]
1777    return [prm for prm in parmList if prm.split(':')[2] not in NonRefinedList]
1778       
1779def getDescr(name):
1780    '''Return a short description for a GSAS-II variable
1781
1782    :param str name: The descriptive part of the variable name without colons (:)
1783
1784    :returns: a short description or None if not found
1785    '''
1786
1787    CompileVarDesc() # compile the regular expressions, if needed
1788    for key in reVarDesc:
1789        m = key.match(name)
1790        if m:
1791            reVarDesc[key]
1792            return m.expand(reVarDesc[key])
1793    return None
1794
1795def getVarStep(name,parmDict=None):
1796    '''Return a step size for computing the derivative of a GSAS-II variable
1797
1798    :param str name: A complete variable name (with colons, :)
1799    :param dict parmDict: A dict with parameter values or None (default)
1800
1801    :returns: a float that should be an appropriate step size, either from
1802      the value supplied in :func:`CompileVarDesc` or based on the value for
1803      name in parmDict, if supplied. If not found or the value is zero,
1804      a default value of 1e-5 is used. If parmDict is None (default) and
1805      no value is provided in :func:`CompileVarDesc`, then None is returned.
1806    '''
1807    CompileVarDesc() # compile the regular expressions, if needed
1808    for key in reVarStep:
1809        m = key.match(name)
1810        if m:
1811            return reVarStep[key]
1812    if parmDict is None: return None
1813    val = parmDict.get(key,0.0)
1814    if abs(val) > 0.05:
1815        return abs(val)/1000.
1816    else:
1817        return 1e-5
1818
1819def GenWildCard(varlist):
1820    '''Generate wildcard versions of G2 variables. These introduce '*'
1821    for a phase, histogram or atom number (but only for one of these
1822    fields) but only when there is more than one matching variable in the
1823    input variable list. So if the input is this::
1824
1825      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
1826
1827    then the output will be this::
1828
1829       wildList = ['*::AUiso:0', '0::AUiso:*']
1830
1831    :param list varlist: an input list of GSAS-II variable names
1832      (such as 0::AUiso:0)
1833
1834    :returns: wildList, the generated list of wild card variable names.
1835    '''
1836    wild = []
1837    for i in (0,1,3):
1838        currentL = varlist[:]
1839        while currentL:
1840            item1 = currentL.pop(0)
1841            i1splt = item1.split(':')
1842            if i >= len(i1splt): continue
1843            if i1splt[i]:
1844                nextL = []
1845                i1splt[i] = '[0-9]+'
1846                rexp = re.compile(':'.join(i1splt))
1847                matchlist = [item1]
1848                for nxtitem in currentL:
1849                    if rexp.match(nxtitem):
1850                        matchlist += [nxtitem]
1851                    else:
1852                        nextL.append(nxtitem)
1853                if len(matchlist) > 1:
1854                    i1splt[i] = '*'
1855                    wild.append(':'.join(i1splt))
1856                currentL = nextL
1857    return wild
1858
1859def LookupWildCard(varname,varlist):
1860    '''returns a list of variable names from list varname
1861    that match wildcard name in varname
1862
1863    :param str varname: a G2 variable name containing a wildcard
1864      (such as \*::var)
1865    :param list varlist: the list of all variable names used in
1866      the current project
1867    :returns: a list of matching GSAS-II variables (may be empty)
1868    '''
1869    rexp = re.compile(varname.replace('*','[0-9]+'))
1870    return sorted([var for var in varlist if rexp.match(var)])
1871
1872
1873def _lookup(dic,key):
1874    '''Lookup a key in a dictionary, where None returns an empty string
1875    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
1876    '''
1877    if key is None:
1878        return ""
1879    elif key == "*":
1880        return "*"
1881    else:
1882        return dic.get(key,'?')
1883
1884def SortVariables(varlist):
1885    '''Sorts variable names in a sensible manner
1886    '''
1887    def cvnnums(var):
1888        v = []
1889        for i in var.split(':'):
1890            if i == '':
1891                v.append(-1)
1892                continue
1893            try:
1894                v.append(int(i))
1895            except:
1896                v.append(i)
1897        return v
1898    return sorted(varlist,key=cvnnums)
1899
1900class G2VarObj(object):
1901    '''Defines a GSAS-II variable either using the phase/atom/histogram
1902    unique Id numbers or using a character string that specifies
1903    variables by phase/atom/histogram number (which can change).
1904    Note that :func:`LoadID` should be used to (re)load the current Ids
1905    before creating or later using the G2VarObj object.
1906
1907    This can store rigid body variables, but does not translate the residue # and
1908    body # to/from random Ids
1909
1910    A :class:`G2VarObj` object can be created with a single parameter:
1911
1912    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
1913      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
1914
1915     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
1916     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
1917     * a is the atom number (which may be left blank in which case the third colon is omitted).
1918       The atom number can be specified as '*' if a phase number is specified (not as '*').
1919       For rigid body variables, specify a will be a string of form "residue:body#"
1920
1921      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
1922      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
1923      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
1924      For a rigid body variables, AtomID is a string of form "residue:body#".
1925
1926    If four positional arguments are supplied, they are:
1927
1928    :param str/int phasenum: The number for the phase (or None or '*')
1929    :param str/int histnum: The number for the histogram (or None or '*')
1930    :param str varname: a single value can be used to create a :class:`G2VarObj`
1931    :param str/int atomnum: The number for the atom (or None or '*')
1932
1933    '''
1934    IDdict = {}
1935    IDdict['phases'] = {}
1936    IDdict['hists'] = {}
1937    IDdict['atoms'] = {}
1938    def __init__(self,*args):
1939        self.phase = None
1940        self.histogram = None
1941        self.name = ''
1942        self.atom = None
1943        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
1944            # single arg with 4 values
1945            self.phase,self.histogram,self.name,self.atom = args[0]
1946        elif len(args) == 1 and ':' in args[0]:
1947            #parse a string
1948            lst = args[0].split(':')
1949            if lst[0] == '*':
1950                self.phase = '*'
1951                if len(lst) > 3:
1952                    self.atom = lst[3]
1953                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1954            elif lst[1] == '*':
1955                self.histogram = '*'
1956                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1957            else:
1958                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1959                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1960                if len(lst) == 4:
1961                    if lst[3] == '*':
1962                        self.atom = '*'
1963                    else:
1964                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
1965                elif len(lst) == 5:
1966                    self.atom = lst[3]+":"+lst[4]
1967                elif len(lst) == 3:
1968                    pass
1969                else:
1970                    raise Exception("Too many colons in var name "+str(args[0]))
1971            self.name = lst[2]
1972        elif len(args) == 4:
1973            if args[0] == '*':
1974                self.phase = '*'
1975                self.atom = args[3]
1976            else:
1977                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
1978                if args[3] == '*':
1979                    self.atom = '*'
1980                elif args[0] is not None:
1981                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
1982            if args[1] == '*':
1983                self.histogram = '*'
1984            else:
1985                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
1986            self.name = args[2]
1987        else:
1988            raise Exception("Incorrectly called GSAS-II parameter name")
1989
1990        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
1991
1992    def __str__(self):
1993        return self.varname()
1994
1995    def varname(self):
1996        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
1997        string (p:h:<var>:a) or (p:h:<var>)
1998
1999        :returns: the variable name as a str
2000        '''
2001        a = ""
2002        if self.phase == "*":
2003            ph = "*"
2004            if self.atom:
2005                a = ":" + str(self.atom)
2006        else:
2007            ph = _lookup(PhaseRanIdLookup,self.phase)
2008            if self.atom == '*':
2009                a = ':*'
2010            elif self.atom:
2011                if ":" in str(self.atom):
2012                    a = ":" + str(self.atom)
2013                elif ph in AtomRanIdLookup:
2014                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
2015                else:
2016                    a = ":?"
2017        if self.histogram == "*":
2018            hist = "*"
2019        else:
2020            hist = _lookup(HistRanIdLookup,self.histogram)
2021        s = (ph + ":" + hist + ":" + str(self.name)) + a
2022        return s
2023
2024    def __repr__(self):
2025        '''Return the detailed contents of the object
2026        '''
2027        s = "<"
2028        if self.phase == '*':
2029            s += "Phases: all; "
2030            if self.atom is not None:
2031                if ":" in str(self.atom):
2032                    s += "Rigid body" + str(self.atom) + "; "
2033                else:
2034                    s += "Atom #" + str(self.atom) + "; "
2035        elif self.phase is not None:
2036            ph =  _lookup(PhaseRanIdLookup,self.phase)
2037            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
2038            if self.atom == '*':
2039                s += "Atoms: all; "
2040            elif ":" in str(self.atom):
2041                s += "Rigid body" + str(self.atom) + "; "
2042            elif self.atom is not None:
2043                s += "Atom rId=" + str(self.atom)
2044                if ph in AtomRanIdLookup:
2045                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
2046                else:
2047                    s += " (#? -- not found!); "
2048        if self.histogram == '*':
2049            s += "Histograms: all; "
2050        elif self.histogram is not None:
2051            hist = _lookup(HistRanIdLookup,self.histogram)
2052            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
2053        s += 'Variable name="' + str(self.name) + '">'
2054        return s+" ("+self.varname()+")"
2055
2056    def __eq__(self, other):
2057        if type(other) is type(self):
2058            return (self.phase == other.phase and
2059                    self.histogram == other.histogram and
2060                    self.name == other.name and
2061                    self.atom == other.atom)
2062        return False
2063
2064    def _show(self):
2065        'For testing, shows the current lookup table'
2066        print ('phases'+ self.IDdict['phases'])
2067        print ('hists'+ self.IDdict['hists'])
2068        print ('atomDict'+ self.IDdict['atoms'])
2069
2070#==========================================================================
2071def SetDefaultSample():
2072    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
2073    return {
2074        'InstrName':'',
2075        'ranId':ran.randint(0,sys.maxsize),
2076        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
2077        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],
2078        'Temperature':300.,'Pressure':0.1,'Time':0.0,
2079        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
2080        'Gonio. radius':200.0,
2081        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
2082#SASD items
2083        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
2084        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
2085        'Trans':1.0,                            #measured transmission
2086        'SlitLen':0.0,                          #Slit length - in Q(A-1)
2087        }
2088######################################################################
2089class ImportBaseclass(object):
2090    '''Defines a base class for the reading of input files (diffraction
2091    data, coordinates,...). See :ref:`Writing a Import Routine<import_routines>`
2092    for an explanation on how to use a subclass of this class.
2093    '''
2094    class ImportException(Exception):
2095        '''Defines an Exception that is used when an import routine hits an expected error,
2096        usually in .Reader.
2097
2098        Good practice is that the Reader should define a value in self.errors that
2099        tells the user some information about what is wrong with their file.
2100        '''
2101        pass
2102
2103    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
2104    def __init__(self,formatName,longFormatName=None,
2105                 extensionlist=[],strictExtension=False,):
2106        self.formatName = formatName # short string naming file type
2107        if longFormatName: # longer string naming file type
2108            self.longFormatName = longFormatName
2109        else:
2110            self.longFormatName = formatName
2111        # define extensions that are allowed for the file type
2112        # for windows, remove any extensions that are duplicate, as case is ignored
2113        if sys.platform == 'windows' and extensionlist:
2114            extensionlist = list(set([s.lower() for s in extensionlist]))
2115        self.extensionlist = extensionlist
2116        # If strictExtension is True, the file will not be read, unless
2117        # the extension matches one in the extensionlist
2118        self.strictExtension = strictExtension
2119        self.errors = ''
2120        self.warnings = ''
2121        self.SciPy = False          #image reader needed scipy
2122        # used for readers that will use multiple passes to read
2123        # more than one data block
2124        self.repeat = False
2125        self.selections = []
2126        self.repeatcount = 0
2127        self.readfilename = '?'
2128        self.scriptable = False
2129        #print 'created',self.__class__
2130
2131    def ReInitialize(self):
2132        'Reinitialize the Reader to initial settings'
2133        self.errors = ''
2134        self.warnings = ''
2135        self.SciPy = False          #image reader needed scipy
2136        self.repeat = False
2137        self.repeatcount = 0
2138        self.readfilename = '?'
2139
2140
2141#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
2142#        '''This method must be supplied in the child class to read the file.
2143#        if the read fails either return False or raise an Exception
2144#        preferably of type ImportException.
2145#        '''
2146#        #start reading
2147#        raise ImportException("Error occurred while...")
2148#        self.errors += "Hint for user on why the error occur
2149#        return False # if an error occurs
2150#        return True # if read OK
2151
2152    def ExtensionValidator(self, filename):
2153        '''This methods checks if the file has the correct extension
2154       
2155        :returns:
2156       
2157          * False if this filename will not be supported by this reader (only
2158            when strictExtension is True)
2159          * True if the extension matches the list supplied by the reader
2160          * None if the reader allows un-registered extensions
2161         
2162        '''
2163        if filename:
2164            ext = ospath.splitext(filename)[1]
2165            if not ext and self.strictExtension: return False
2166            for ext in self.extensionlist:               
2167                if sys.platform == 'windows':
2168                    if filename.lower().endswith(ext): return True
2169                else:
2170                    if filename.endswith(ext): return True
2171        if self.strictExtension:
2172            return False
2173        else:
2174            return None
2175
2176    def ContentsValidator(self, filename):
2177        '''This routine will attempt to determine if the file can be read
2178        with the current format.
2179        This will typically be overridden with a method that
2180        takes a quick scan of [some of]
2181        the file contents to do a "sanity" check if the file
2182        appears to match the selected format.
2183        the file must be opened here with the correct format (binary/text)
2184        '''
2185        #filepointer.seek(0) # rewind the file pointer
2186        return True
2187
2188    def CIFValidator(self, filepointer):
2189        '''A :meth:`ContentsValidator` for use to validate CIF files.
2190        '''
2191        filepointer.seek(0)
2192        for i,l in enumerate(filepointer):
2193            if i >= 1000: return True
2194            '''Encountered only blank lines or comments in first 1000
2195            lines. This is unlikely, but assume it is CIF anyway, since we are
2196            even less likely to find a file with nothing but hashes and
2197            blank lines'''
2198            line = l.strip()
2199            if len(line) == 0: # ignore blank lines
2200                continue
2201            elif line.startswith('#'): # ignore comments
2202                continue
2203            elif line.startswith('data_'): # on the right track, accept this file
2204                return True
2205            else: # found something invalid
2206                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
2207                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
2208                    self.errors += '  '+str(l)
2209                else:
2210                    self.errors += '  (binary)'
2211                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
2212                self.errors += '\n        a data_ statement begins a block.'
2213                return False
2214
2215######################################################################
2216class ImportPhase(ImportBaseclass):
2217    '''Defines a base class for the reading of files with coordinates
2218
2219    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
2220    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` and in
2221    :func:`GSASIIscriptable.import_generic`.
2222    See :ref:`Writing a Import Routine<import_routines>`
2223    for an explanation on how to use this class.
2224
2225    '''
2226    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2227        strictExtension=False,):
2228        # call parent __init__
2229        ImportBaseclass.__init__(self,formatName,longFormatName,
2230            extensionlist,strictExtension)
2231        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
2232        self.Constraints = None
2233
2234######################################################################
2235class ImportStructFactor(ImportBaseclass):
2236    '''Defines a base class for the reading of files with tables
2237    of structure factors.
2238
2239    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
2240    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
2241    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2242    :meth:`Reader`.
2243
2244    See :ref:`Writing a Import Routine<import_routines>`
2245    for an explanation on how to use import classes in general. The specifics
2246    for reading a structure factor histogram require that
2247    the ``Reader()`` routine in the import
2248    class need to do only a few things: It
2249    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2250    and set :attr:`Parameters` with the instrument parameters
2251    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2252    '''
2253    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2254        strictExtension=False,):
2255        ImportBaseclass.__init__(self,formatName,longFormatName,
2256            extensionlist,strictExtension)
2257
2258        # define contents of Structure Factor entry
2259        self.Parameters = []
2260        'self.Parameters is a list with two dicts for data parameter settings'
2261        self.InitParameters()
2262        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2263        self.Banks = []             #for multi bank data (usually TOF)
2264        '''self.RefDict is a dict containing the reflection information, as read from the file.
2265        Item 'RefList' contains the reflection information. See the
2266        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
2267        for the contents of each row. Dict element 'FF'
2268        contains the form factor values for each element type; if this entry
2269        is left as initialized (an empty list) it will be initialized as needed later.
2270        '''
2271    def ReInitialize(self):
2272        'Reinitialize the Reader to initial settings'
2273        ImportBaseclass.ReInitialize(self)
2274        self.InitParameters()
2275        self.Banks = []             #for multi bank data (usually TOF)
2276        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2277
2278    def InitParameters(self):
2279        'initialize the instrument parameters structure'
2280        Lambda = 0.70926
2281        HistType = 'SXC'
2282        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2283                            'Lam':[Lambda,Lambda]
2284                            }, {}]
2285        'Parameters is a list with two dicts for data parameter settings'
2286
2287    def UpdateParameters(self,Type=None,Wave=None):
2288        'Revise the instrument parameters'
2289        if Type is not None:
2290            self.Parameters[0]['Type'] = [Type,Type]
2291        if Wave is not None:
2292            self.Parameters[0]['Lam'] = [Wave,Wave]
2293
2294######################################################################
2295class ImportPowderData(ImportBaseclass):
2296    '''Defines a base class for the reading of files with powder data.
2297
2298    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2299    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder` and in
2300    :func:`GSASIIscriptable.import_generic`.
2301    See :ref:`Writing a Import Routine<import_routines>`
2302    for an explanation on how to use this class.
2303    '''
2304    def __init__(self,formatName,longFormatName=None,
2305        extensionlist=[],strictExtension=False,):
2306        ImportBaseclass.__init__(self,formatName,longFormatName,
2307            extensionlist,strictExtension)
2308        self.clockWd = None  # used in TOF
2309        self.ReInitialize()
2310
2311    def ReInitialize(self):
2312        'Reinitialize the Reader to initial settings'
2313        ImportBaseclass.ReInitialize(self)
2314        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2315        self.powderdata = [] # Powder dataset
2316        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2317                np.array(x), # x-axis values
2318                np.array(y), # powder pattern intensities
2319                np.array(w), # 1/sig(intensity)^2 values (weights)
2320                np.array(yc), # calc. intensities (zero)
2321                np.array(yb), # calc. background (zero)
2322                np.array(yd), # obs-calc profiles
2323        '''
2324        self.comments = []
2325        self.idstring = ''
2326        self.Sample = SetDefaultSample() # default sample parameters
2327        self.Controls = {}  # items to be placed in top-level Controls
2328        self.GSAS = None     # used in TOF
2329        self.repeat_instparm = True # Should a parm file be
2330        #                             used for multiple histograms?
2331        self.instparm = None # name hint from file of instparm to use
2332        self.instfile = '' # full path name to instrument parameter file
2333        self.instbank = '' # inst parm bank number
2334        self.instmsg = ''  # a label that gets printed to show
2335                           # where instrument parameters are from
2336        self.numbanks = 1
2337        self.instdict = {} # place items here that will be transferred to the instrument parameters
2338        self.pwdparms = {} # place parameters that are transferred directly to the tree
2339                           # here (typically from an existing GPX file)
2340######################################################################
2341class ImportSmallAngleData(ImportBaseclass):
2342    '''Defines a base class for the reading of files with small angle data.
2343    See :ref:`Writing a Import Routine<import_routines>`
2344    for an explanation on how to use this class.
2345    '''
2346    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2347        strictExtension=False,):
2348
2349        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2350            strictExtension)
2351        self.ReInitialize()
2352
2353    def ReInitialize(self):
2354        'Reinitialize the Reader to initial settings'
2355        ImportBaseclass.ReInitialize(self)
2356        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2357        self.smallangledata = [] # SASD dataset
2358        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2359                np.array(x), # x-axis values
2360                np.array(y), # powder pattern intensities
2361                np.array(w), # 1/sig(intensity)^2 values (weights)
2362                np.array(yc), # calc. intensities (zero)
2363                np.array(yd), # obs-calc profiles
2364                np.array(yb), # preset bkg
2365        '''
2366        self.comments = []
2367        self.idstring = ''
2368        self.Sample = SetDefaultSample()
2369        self.GSAS = None     # used in TOF
2370        self.clockWd = None  # used in TOF
2371        self.numbanks = 1
2372        self.instdict = {} # place items here that will be transferred to the instrument parameters
2373
2374######################################################################
2375class ImportReflectometryData(ImportBaseclass):
2376    '''Defines a base class for the reading of files with reflectometry data.
2377    See :ref:`Writing a Import Routine<import_routines>`
2378    for an explanation on how to use this class.
2379    '''
2380    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2381        strictExtension=False,):
2382
2383        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2384            strictExtension)
2385        self.ReInitialize()
2386
2387    def ReInitialize(self):
2388        'Reinitialize the Reader to initial settings'
2389        ImportBaseclass.ReInitialize(self)
2390        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2391        self.reflectometrydata = [] # SASD dataset
2392        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2393                np.array(x), # x-axis values
2394                np.array(y), # powder pattern intensities
2395                np.array(w), # 1/sig(intensity)^2 values (weights)
2396                np.array(yc), # calc. intensities (zero)
2397                np.array(yd), # obs-calc profiles
2398                np.array(yb), # preset bkg
2399        '''
2400        self.comments = []
2401        self.idstring = ''
2402        self.Sample = SetDefaultSample()
2403        self.GSAS = None     # used in TOF
2404        self.clockWd = None  # used in TOF
2405        self.numbanks = 1
2406        self.instdict = {} # place items here that will be transferred to the instrument parameters
2407
2408######################################################################
2409class ImportPDFData(ImportBaseclass):
2410    '''Defines a base class for the reading of files with PDF G(R) data.
2411    See :ref:`Writing a Import Routine<import_routines>`
2412    for an explanation on how to use this class.
2413    '''
2414    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2415        strictExtension=False,):
2416
2417        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2418            strictExtension)
2419        self.ReInitialize()
2420
2421    def ReInitialize(self):
2422        'Reinitialize the Reader to initial settings'
2423        ImportBaseclass.ReInitialize(self)
2424        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2425        self.pdfdata = [] # PDF G(R) dataset
2426        '''A pdf g(r) data set is a list with items [x,y]:
2427                np.array(x), # r-axis values
2428                np.array(y), # pdf g(r)
2429        '''
2430        self.comments = []
2431        self.idstring = ''
2432        self.numbanks = 1
2433
2434######################################################################
2435class ImportImage(ImportBaseclass):
2436    '''Defines a base class for the reading of images
2437
2438    Images are read in only these places:
2439
2440      * Initial reading is typically done from a menu item
2441        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2442        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2443        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2444        :meth:`Reader`. This returns a list of reader objects for each read image.
2445        Also used in :func:`GSASIIscriptable.import_generic`.
2446
2447      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2448        directly into the data tree.
2449
2450      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2451
2452    When reading an image, the ``Reader()`` routine in the ImportImage class
2453    should set:
2454
2455      * :attr:`Comments`: a list of strings (str),
2456      * :attr:`Npix`: the number of pixels in the image (int),
2457      * :attr:`Image`: the actual image as a numpy array (np.array)
2458      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2459        data items are needed:
2460
2461         * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2462         * 'wavelength': wavelength in :math:`\\AA`.
2463         * 'distance': distance of detector from sample in cm.
2464         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2465         * 'size': size of image (such as ``[2048,2048]``).
2466         * 'ImageTag': image number or other keyword used to retrieve image from
2467           a multi-image data file (defaults to ``1`` if not specified).
2468         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2469
2470    optional data items:
2471
2472      * :attr:`repeat`: set to True if there are additional images to
2473        read in the file, False otherwise
2474      * :attr:`repeatcount`: set to the number of the image.
2475
2476    Note that the above is initialized with :meth:`InitParameters`.
2477    (Also see :ref:`Writing a Import Routine<import_routines>`
2478    for an explanation on how to use import classes in general.)
2479    '''
2480    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2481        strictExtension=False,):
2482        ImportBaseclass.__init__(self,formatName,longFormatName,
2483            extensionlist,strictExtension)
2484        self.InitParameters()
2485
2486    def ReInitialize(self):
2487        'Reinitialize the Reader to initial settings -- not used at present'
2488        ImportBaseclass.ReInitialize(self)
2489        self.InitParameters()
2490
2491    def InitParameters(self):
2492        'initialize the instrument parameters structure'
2493        self.Comments = ['No comments']
2494        self.Data = {}
2495        self.Npix = 0
2496        self.Image = None
2497        self.repeat = False
2498        self.repeatcount = 1
2499        self.sumfile = ''
2500
2501    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2502        '''Optionally, call this after reading in an image to load it into the tree.
2503        This saves time by preventing a reread of the same information.
2504        '''
2505        if ParentFrame:
2506            ParentFrame.ImageZ = self.Image   # store the image for plotting
2507            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2508            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2509
2510#################################################################################################
2511# shortcut routines
2512exp = np.exp
2513sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2514cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2515tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2516sqrt = sq = lambda x: np.sqrt(x)
2517pi = lambda: np.pi
2518class ExpressionObj(object):
2519    '''Defines an object with a user-defined expression, to be used for
2520    secondary fits or restraints. Object is created null, but is changed
2521    using :meth:`LoadExpression`. This contains only the minimum
2522    information that needs to be stored to save and load the expression
2523    and how it is mapped to GSAS-II variables.
2524    '''
2525    def __init__(self):
2526        self.expression = ''
2527        'The expression as a text string'
2528        self.assgnVars = {}
2529        '''A dict where keys are label names in the expression mapping to a GSAS-II
2530        variable. The value a G2 variable name.
2531        Note that the G2 variable name may contain a wild-card and correspond to
2532        multiple values.
2533        '''
2534        self.freeVars = {}
2535        '''A dict where keys are label names in the expression mapping to a free
2536        parameter. The value is a list with:
2537
2538         * a name assigned to the parameter
2539         * a value for to the parameter and
2540         * a flag to determine if the variable is refined.
2541        '''
2542        self.depVar = None
2543
2544        self.lastError = ('','')
2545        '''Shows last encountered error in processing expression
2546        (list of 1-3 str values)'''
2547
2548        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2549        self.distance_atoms = None  # to be used for defining atom distances
2550
2551    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2552        '''Load the expression and associated settings into the object. Raises
2553        an exception if the expression is not parsed, if not all functions
2554        are defined or if not all needed parameter labels in the expression
2555        are defined.
2556
2557        This will not test if the variable referenced in these definitions
2558        are actually in the parameter dictionary. This is checked when the
2559        computation for the expression is done in :meth:`SetupCalc`.
2560
2561        :param str expr: the expression
2562        :param list exprVarLst: parameter labels found in the expression
2563        :param dict varSelect: this will be 0 for Free parameters
2564          and non-zero for expression labels linked to G2 variables.
2565        :param dict varName: Defines a name (str) associated with each free parameter
2566        :param dict varValue: Defines a value (float) associated with each free parameter
2567        :param dict varRefflag: Defines a refinement flag (bool)
2568          associated with each free parameter
2569        '''
2570        self.expression = expr
2571        self.compiledExpr = None
2572        self.freeVars = {}
2573        self.assgnVars = {}
2574        for v in exprVarLst:
2575            if varSelect[v] == 0:
2576                self.freeVars[v] = [
2577                    varName.get(v),
2578                    varValue.get(v),
2579                    varRefflag.get(v),
2580                    ]
2581            else:
2582                self.assgnVars[v] = varName[v]
2583        self.CheckVars()
2584
2585    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2586        '''Load the expression and associated settings from the object into
2587        arrays used for editing.
2588
2589        :param list exprVarLst: parameter labels found in the expression
2590        :param dict varSelect: this will be 0 for Free parameters
2591          and non-zero for expression labels linked to G2 variables.
2592        :param dict varName: Defines a name (str) associated with each free parameter
2593        :param dict varValue: Defines a value (float) associated with each free parameter
2594        :param dict varRefflag: Defines a refinement flag (bool)
2595          associated with each free parameter
2596
2597        :returns: the expression as a str
2598        '''
2599        for v in self.freeVars:
2600            varSelect[v] = 0
2601            varName[v] = self.freeVars[v][0]
2602            varValue[v] = self.freeVars[v][1]
2603            varRefflag[v] = self.freeVars[v][2]
2604        for v in self.assgnVars:
2605            varSelect[v] = 1
2606            varName[v] = self.assgnVars[v]
2607        return self.expression
2608
2609    def GetVaried(self):
2610        'Returns the names of the free parameters that will be refined'
2611        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
2612
2613    def GetVariedVarVal(self):
2614        'Returns the names and values of the free parameters that will be refined'
2615        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
2616
2617    def UpdateVariedVars(self,varyList,values):
2618        'Updates values for the free parameters (after a refinement); only updates refined vars'
2619        for v in self.freeVars:
2620            if not self.freeVars[v][2]: continue
2621            if "::"+self.freeVars[v][0] not in varyList: continue
2622            indx = list(varyList).index("::"+self.freeVars[v][0])
2623            self.freeVars[v][1] = values[indx]
2624
2625    def GetIndependentVars(self):
2626        'Returns the names of the required independent parameters used in expression'
2627        return [self.assgnVars[v] for v in self.assgnVars]
2628
2629    def CheckVars(self):
2630        '''Check that the expression can be parsed, all functions are
2631        defined and that input loaded into the object is internally
2632        consistent. If not an Exception is raised.
2633
2634        :returns: a dict with references to packages needed to
2635          find functions referenced in the expression.
2636        '''
2637        ret = self.ParseExpression(self.expression)
2638        if not ret:
2639            raise Exception("Expression parse error")
2640        exprLblList,fxnpkgdict = ret
2641        # check each var used in expression is defined
2642        defined = list(self.assgnVars.keys()) + list(self.freeVars.keys())
2643        notfound = []
2644        for var in exprLblList:
2645            if var not in defined:
2646                notfound.append(var)
2647        if notfound:
2648            msg = 'Not all variables defined'
2649            msg1 = 'The following variables were not defined: '
2650            msg2 = ''
2651            for var in notfound:
2652                if msg: msg += ', '
2653                msg += var
2654            self.lastError = (msg1,'  '+msg2)
2655            raise Exception(msg)
2656        return fxnpkgdict
2657
2658    def ParseExpression(self,expr):
2659        '''Parse an expression and return a dict of called functions and
2660        the variables used in the expression. Returns None in case an error
2661        is encountered. If packages are referenced in functions, they are loaded
2662        and the functions are looked up into the modules global
2663        workspace.
2664
2665        Note that no changes are made to the object other than
2666        saving an error message, so that this can be used for testing prior
2667        to the save.
2668
2669        :returns: a list of used variables
2670        '''
2671        self.lastError = ('','')
2672        import ast
2673        def FindFunction(f):
2674            '''Find the object corresponding to function f
2675            :param str f: a function name such as 'numpy.exp'
2676            :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2677              that defines the package location(s) and where pkgobj
2678              defines the object associated with the function.
2679              If the function is not found, pkgobj is None.
2680            '''
2681            df = f.split('.')
2682            pkgdict = {}
2683            # no listed package, try in current namespace
2684            if len(df) == 1:
2685                try:
2686                    fxnobj = eval(f)
2687                    return pkgdict,fxnobj
2688                except (AttributeError, NameError):
2689                    return None,None
2690            else:
2691                try:
2692                    fxnobj = eval(f)
2693                    pkgdict[df[0]] = eval(df[0])
2694                    return pkgdict,fxnobj
2695                except (AttributeError, NameError):
2696                    pass
2697            # includes a package, lets try to load the packages
2698            pkgname = ''
2699            path = sys.path+['./',]
2700            for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2701                if pkgname:
2702                    pkgname += '.' + pkg
2703                else:
2704                    pkgname = pkg
2705                fp = None
2706                try:
2707                    fp, fppath,desc = imp.find_module(pkg,path)
2708                    pkgobj = imp.load_module(pkg,fp,fppath,desc)
2709                    pkgdict[pkgname] = pkgobj
2710                    path = [fppath]
2711                except Exception as msg:
2712                    print('load of '+pkgname+' failed with error='+str(msg))
2713                    return {},None
2714                finally:
2715                    if fp: fp.close()
2716                try:
2717                    #print 'before',pkgdict.keys()
2718                    fxnobj = eval(f,globals(),pkgdict)
2719                    #print 'after 1',pkgdict.keys()
2720                    #fxnobj = eval(f,pkgdict)
2721                    #print 'after 2',pkgdict.keys()
2722                    return pkgdict,fxnobj
2723                except:
2724                    continue
2725            return None # not found
2726        def ASTtransverse(node,fxn=False):
2727            '''Transverse a AST-parsed expresson, compiling a list of variables
2728            referenced in the expression. This routine is used recursively.
2729
2730            :returns: varlist,fxnlist where
2731              varlist is a list of referenced variable names and
2732              fxnlist is a list of used functions
2733            '''
2734            varlist = []
2735            fxnlist = []
2736            if isinstance(node, list):
2737                for b in node:
2738                    v,f = ASTtransverse(b,fxn)
2739                    varlist += v
2740                    fxnlist += f
2741            elif isinstance(node, ast.AST):
2742                for a, b in ast.iter_fields(node):
2743                    if isinstance(b, ast.AST):
2744                        if a == 'func':
2745                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
2746                            continue
2747                        v,f = ASTtransverse(b,fxn)
2748                        varlist += v
2749                        fxnlist += f
2750                    elif isinstance(b, list):
2751                        v,f = ASTtransverse(b,fxn)
2752                        varlist += v
2753                        fxnlist += f
2754                    elif node.__class__.__name__ == "Name":
2755                        varlist += [b]
2756                    elif fxn and node.__class__.__name__ == "Attribute":
2757                        varlist += [b]
2758            return varlist,fxnlist
2759        try:
2760            exprast = ast.parse(expr)
2761        except SyntaxError:
2762            s = ''
2763            import traceback
2764            for i in traceback.format_exc().splitlines()[-3:-1]:
2765                if s: s += "\n"
2766                s += str(i)
2767            self.lastError = ("Error parsing expression:",s)
2768            return
2769        # find the variables & functions
2770        v,f = ASTtransverse(exprast)
2771        varlist = sorted(list(set(v)))
2772        fxnlist = list(set(f))
2773        pkgdict = {}
2774        # check the functions are defined
2775        for fxn in fxnlist:
2776            fxndict,fxnobj = FindFunction(fxn)
2777            if not fxnobj:
2778                self.lastError = ("Error: Invalid function",fxn,
2779                                  "is not defined")
2780                return
2781            if not hasattr(fxnobj,'__call__'):
2782                self.lastError = ("Error: Not a function.",fxn,
2783                                  "cannot be called as a function")
2784                return
2785            pkgdict.update(fxndict)
2786        return varlist,pkgdict
2787
2788    def GetDepVar(self):
2789        'return the dependent variable, or None'
2790        return self.depVar
2791
2792    def SetDepVar(self,var):
2793        'Set the dependent variable, if used'
2794        self.depVar = var
2795#==========================================================================
2796class ExpressionCalcObj(object):
2797    '''An object used to evaluate an expression from a :class:`ExpressionObj`
2798    object.
2799
2800    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
2801      an expression string and mappings for the parameter labels in that object.
2802    '''
2803    def __init__(self,exprObj):
2804        self.eObj = exprObj
2805        'The expression and mappings; a :class:`ExpressionObj` object'
2806        self.compiledExpr = None
2807        'The expression as compiled byte-code'
2808        self.exprDict = {}
2809        '''dict that defines values for labels used in expression and packages
2810        referenced by functions
2811        '''
2812        self.lblLookup = {}
2813        '''Lookup table that specifies the expression label name that is
2814        tied to a particular GSAS-II parameters in the parmDict.
2815        '''
2816        self.fxnpkgdict = {}
2817        '''a dict with references to packages needed to
2818        find functions referenced in the expression.
2819        '''
2820        self.varLookup = {}
2821        '''Lookup table that specifies the GSAS-II variable(s)
2822        indexed by the expression label name. (Used for only for diagnostics
2823        not evaluation of expression.)
2824        '''
2825        self.su = None
2826        '''Standard error evaluation where supplied by the evaluator
2827        '''
2828        # Patch: for old-style expressions with a (now removed step size)
2829        if '2' in platform.python_version_tuple()[0]: 
2830            basestr = basestring
2831        else:
2832            basestr = str
2833        for v in self.eObj.assgnVars:
2834            if not isinstance(self.eObj.assgnVars[v], basestr):
2835                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
2836        self.parmDict = {}
2837        '''A copy of the parameter dictionary, for distance and angle computation
2838        '''
2839
2840    def SetupCalc(self,parmDict):
2841        '''Do all preparations to use the expression for computation.
2842        Adds the free parameter values to the parameter dict (parmDict).
2843        '''
2844        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2845            return
2846        self.fxnpkgdict = self.eObj.CheckVars()
2847        # all is OK, compile the expression
2848        self.compiledExpr = compile(self.eObj.expression,'','eval')
2849
2850        # look at first value in parmDict to determine its type
2851        parmsInList = True
2852        if '2' in platform.python_version_tuple()[0]: 
2853            basestr = basestring
2854        else:
2855            basestr = str
2856        for key in parmDict:
2857            val = parmDict[key]
2858            if isinstance(val, basestr):
2859                parmsInList = False
2860                break
2861            try: # check if values are in lists
2862                val = parmDict[key][0]
2863            except (TypeError,IndexError):
2864                parmsInList = False
2865            break
2866
2867        # set up the dicts needed to speed computations
2868        self.exprDict = {}
2869        self.lblLookup = {}
2870        self.varLookup = {}
2871        for v in self.eObj.freeVars:
2872            varname = self.eObj.freeVars[v][0]
2873            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
2874            self.lblLookup[varname] = v
2875            self.varLookup[v] = varname
2876            if parmsInList:
2877                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
2878            else:
2879                parmDict[varname] = self.eObj.freeVars[v][1]
2880            self.exprDict[v] = self.eObj.freeVars[v][1]
2881        for v in self.eObj.assgnVars:
2882            varname = self.eObj.assgnVars[v]
2883            if varname in parmDict:
2884                self.lblLookup[varname] = v
2885                self.varLookup[v] = varname
2886                if parmsInList:
2887                    self.exprDict[v] = parmDict[varname][0]
2888                else:
2889                    self.exprDict[v] = parmDict[varname]
2890            elif '*' in varname:
2891                varlist = LookupWildCard(varname,list(parmDict.keys()))
2892                if len(varlist) == 0:
2893                    raise Exception("No variables match "+str(v))
2894                for var in varlist:
2895                    self.lblLookup[var] = v
2896                if parmsInList:
2897                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
2898                else:
2899                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
2900                self.varLookup[v] = [var for var in varlist]
2901            else:
2902                self.exprDict[v] = None
2903#                raise Exception,"No value for variable "+str(v)
2904        self.exprDict.update(self.fxnpkgdict)
2905
2906    def UpdateVars(self,varList,valList):
2907        '''Update the dict for the expression with a set of values
2908        :param list varList: a list of variable names
2909        :param list valList: a list of corresponding values
2910        '''
2911        for var,val in zip(varList,valList):
2912            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
2913
2914    def UpdateDict(self,parmDict):
2915        '''Update the dict for the expression with values in a dict
2916        :param dict parmDict: a dict of values, items not in use are ignored
2917        '''
2918        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2919            self.parmDict = parmDict
2920            return
2921        for var in parmDict:
2922            if var in self.lblLookup:
2923                self.exprDict[self.lblLookup[var]] = parmDict[var]
2924
2925    def EvalExpression(self):
2926        '''Evaluate an expression. Note that the expression
2927        and mapping are taken from the :class:`ExpressionObj` expression object
2928        and the parameter values were specified in :meth:`SetupCalc`.
2929        :returns: a single value for the expression. If parameter
2930        values are arrays (for example, from wild-carded variable names),
2931        the sum of the resulting expression is returned.
2932
2933        For example, if the expression is ``'A*B'``,
2934        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
2935
2936        [0.5, 1, 0.5]
2937
2938        then the result will be ``4.0``.
2939        '''
2940        self.su = None
2941        if self.eObj.expression.startswith('Dist'):
2942#            GSASIIpath.IPyBreak()
2943            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
2944            return dist
2945        elif self.eObj.expression.startswith('Angle'):
2946            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
2947            return angle
2948        if self.compiledExpr is None:
2949            raise Exception("EvalExpression called before SetupCalc")
2950        try:
2951            val = eval(self.compiledExpr,globals(),self.exprDict)
2952        except TypeError:
2953            val = None
2954        if not np.isscalar(val):
2955            val = np.sum(val)
2956        return val
2957
2958class G2Exception(Exception):
2959    'A generic GSAS-II exception class'
2960    def __init__(self,msg):
2961        self.msg = msg
2962    def __str__(self):
2963        return repr(self.msg)
2964
2965class G2RefineCancel(Exception):
2966    'Raised when Cancel is pressed in a refinement dialog'
2967    def __init__(self,msg):
2968        self.msg = msg
2969    def __str__(self):
2970        return repr(self.msg)
2971   
2972def HowDidIgetHere(wherecalledonly=False):
2973    '''Show a traceback with calls that brought us to the current location.
2974    Used for debugging.
2975    '''
2976    import traceback
2977    if wherecalledonly:
2978        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
2979        print(i.strip().rstrip())
2980    else:
2981        print (70*'*')
2982        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
2983        print (70*'*')
2984
2985# Note that this is GUI code and should be moved at somepoint
2986def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
2987    '''Create and initialize a new set of PDF tree entries
2988
2989    :param Frame G2frame: main GSAS-II tree frame object
2990    :param str PWDRtree: name of PWDR to be used to create PDF item
2991    :param dict ElList: data structure with composition
2992    :param list Qlimits: Q limits to be used for computing the PDF
2993    :param float numAtm: no. atom in chemical formula
2994    :param float FltBkg: flat background value
2995    :param list PDFnames: previously used PDF names
2996
2997    :returns: the Id of the newly created PDF entry
2998    '''
2999    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
3000    if PDFname in PDFnames:
3001        print('Skipping, entry already exists: '+PDFname)
3002        return None
3003    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
3004    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
3005    Data = {
3006        'Sample':{'Name':PWDRtree,'Mult':1.0},
3007        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
3008        'Container':{'Name':'','Mult':-1.0,'Refine':False},
3009        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
3010        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
3011        'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
3012        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,'Rmin':1.0,
3013        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
3014    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
3015    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
3016        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
3017    return Id
3018#%%
3019class ShowTiming(object):
3020    '''An object to use for timing repeated sections of code.
3021
3022    Create the object with::
3023       tim0 = ShowTiming()
3024
3025    Tag sections of code to be timed with::
3026       tim0.start('start')
3027       tim0.start('in section 1')
3028       tim0.start('in section 2')
3029       
3030    etc. (Note that each section should have a unique label.)
3031
3032    After the last section, end timing with::
3033       tim0.end()
3034
3035    Show timing results with::
3036       tim0.show()
3037       
3038    '''
3039    def __init__(self):
3040        self.timeSum =  []
3041        self.timeStart = []
3042        self.label = []
3043        self.prev = None
3044    def start(self,label):
3045        import time
3046        if label in self.label:
3047            i = self.label.index(label)
3048            self.timeStart[i] = time.time()
3049        else:
3050            i = len(self.label)
3051            self.timeSum.append(0.0)
3052            self.timeStart.append(time.time())
3053            self.label.append(label)
3054        if self.prev is not None:
3055            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
3056        self.prev = i
3057    def end(self):
3058        import time
3059        if self.prev is not None:
3060            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
3061        self.prev = None
3062    def show(self):
3063        sumT = sum(self.timeSum)
3064        print('Timing results (total={:.2f} sec)'.format(sumT))
3065        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
3066            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
3067#%%
3068
3069if __name__ == "__main__":
3070    # test variable descriptions
3071    for var in '0::Afrac:*',':1:Scale','1::dAx:0','::undefined':
3072        v = var.split(':')[2]
3073        print(var+':\t', getDescr(v),getVarStep(v))
3074    import sys; sys.exit()
3075    # test equation evaluation
3076    def showEQ(calcobj):
3077        print (50*'=')
3078        print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
3079        for v in sorted(calcobj.varLookup):
3080            print ("  "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
3081        # print '  Derivatives'
3082        # for v in calcobj.derivStep.keys():
3083        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
3084
3085    obj = ExpressionObj()
3086
3087    obj.expression = "A*np.exp(B)"
3088    obj.assgnVars =  {'B': '0::Afrac:1'}
3089    obj.freeVars =  {'A': [u'A', 0.5, True]}
3090    #obj.CheckVars()
3091    calcobj = ExpressionCalcObj(obj)
3092
3093    obj1 = ExpressionObj()
3094    obj1.expression = "A*np.exp(B)"
3095    obj1.assgnVars =  {'B': '0::Afrac:*'}
3096    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
3097    #obj.CheckVars()
3098    calcobj1 = ExpressionCalcObj(obj1)
3099
3100    obj2 = ExpressionObj()
3101    obj2.distance_stuff = np.array([[0,1],[1,-1]])
3102    obj2.expression = "Dist(1,2)"
3103    GSASIIpath.InvokeDebugOpts()
3104    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3105    calcobj2 = ExpressionCalcObj(obj2)
3106    calcobj2.SetupCalc(parmDict2)
3107    showEQ(calcobj2)
3108
3109    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
3110    print ('\nDict = '+parmDict1)
3111    calcobj.SetupCalc(parmDict1)
3112    showEQ(calcobj)
3113    calcobj1.SetupCalc(parmDict1)
3114    showEQ(calcobj1)
3115
3116    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3117    print ('Dict = '+parmDict2)
3118    calcobj.SetupCalc(parmDict2)
3119    showEQ(calcobj)
3120    calcobj1.SetupCalc(parmDict2)
3121    showEQ(calcobj1)
3122    calcobj2.SetupCalc(parmDict2)
3123    showEQ(calcobj2)
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