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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2021-09-30 13:12:56 +0000 (Thu, 30 Sep 2021) $
5# $Author: vondreele $
6# $Revision: 5041 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 5041 2021-09-30 13:12:56Z vondreele $
9########### SVN repository information ###################
10
11'''
12*GSASIIobj: Data objects*
13=========================
14
15This module defines and/or documents the data structures used in GSAS-II, as well
16as provides misc. support routines.
17
18.. Next command allows \\AA to be used in HTML
19
20.. only:: html
21
22   :math:`\\require{mediawiki-texvc}`
23
24.. _Constraints_table:
25
26.. index::
27   single: Constraints object description
28   single: Data object descriptions; Constraints
29
30Constraints Tree Item
31----------------------
32
33Constraints are stored in a dict, separated into groups.
34Note that parameter are named in the following pattern,
35p:h:<var>:n, where p is the phase number, h is the histogram number
36<var> is a variable name and n is the parameter number.
37If a parameter does not depend on a histogram or phase or is unnumbered, that
38number is omitted.
39Note that the contents of each dict item is a List where each element in the
40list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
41The constraints in this form are converted in
42:func:`GSASIImapvars.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
315MCSA            \\               (dict) Monte-Carlo simulated annealing parameters
316==========  ===============     =====================================================================================================
317
318.. _RBData_table:
319
320.. index::
321   single: Rigid Body Data description
322   single: Data object descriptions; Rigid Body Data
323
324Rigid Body Objects
325------------------
326
327Rigid body descriptions are available for two types of rigid bodies: 'Vector'
328and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
329with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
330with defined refinable torsion angles.
331
332.. tabularcolumns:: |l|l|p{4in}|
333
334==========  ===============     ====================================================
335  key         sub-key           explanation
336==========  ===============     ====================================================
337Vector      RBId                (dict of dict) vector rigid bodies
338\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
339\\           RBname              (str) Name assigned by user to rigid body
340\\           VectMag             (list) vector magnitudes in :math:`\\AA`
341\\           rbXYZ               (list of 3 float Cartesian coordinates for Vector rigid body )
342\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
343                                definition, use center of atoms flag
344\\           VectRef             (list of bool refinement flags for VectMag values )
345\\           rbTypes             (list of str) Atom types for each atom in rigid body
346\\           rbVect              (list of lists) Cartesian vectors for each translation used to build rigid body
347\\           useCount            (int) Number of times rigid body is used in any structure
348Residue     RBId                (dict of dict) residue rigid bodies
349\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
350\\           RBname              (str) Name assigned by user to rigid body
351\\           rbXYZ               (list of 3 float) Cartesian coordinates for Residue rigid body
352\\           rbTypes             (list of str) Atom types for each atom in rigid body
353\\           atNames             (list of str) Names of each atom in rigid body (e.g. C1,N2...)
354\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
355                                definition, use center of atoms flag
356\\           rbSeq               (list) Orig,Piv,angle,Riding : definition of internal rigid body
357                                torsion; origin atom (int), pivot atom (int), torsion angle (float),
358                                riding atoms (list of int)
359\\           SelSeq              (int,int) used by SeqSizer to identify objects
360\\           useCount            (int)Number of times rigid body is used in any structure
361RBIds           \\               (dict) unique Ids generated upon creation of each rigid body
362\\           Vector              (list) Ids for each Vector rigid body
363\\           Residue             (list) Ids for each Residue rigid body
364==========  ===============     ====================================================
365
366.. _SGData_table:
367
368.. index::
369   single: Space Group Data description
370   single: Data object descriptions; Space Group Data
371
372Space Group Objects
373-------------------
374
375Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
376and the information is placed in a SGdata object
377which is a dict with these keys. Magnetic ones are marked "mag"
378
379.. tabularcolumns:: |l|p{4.5in}|
380
381==========  ========================================================================================
382  key         explanation
383==========  ========================================================================================
384BNSlattsym  mag - (str) BNS magnetic space group symbol and centering vector
385GenFlg      mag - (list) symmetry generators indices
386GenSym      mag - (list) names for each generator
387MagMom      mag - (list) "time reversals" for each magnetic operator
388MagPtGp     mag - (str) Magnetic point group symbol
389MagSpGrp    mag - (str) Magnetic space group symbol
390OprNames    mag - (list) names for each space group operation
391SGCen       (np.array) Symmetry cell centering vectors. A (n,3) np.array
392            of centers. Will always have at least one row: ``np.array([[0, 0, 0]])``
393SGFixed     (bool) Only True if phase mported from a magnetic cif file
394            then the space group can not be changed by the user because
395            operator set from cif may be nonstandard
396SGGen       (list) generators
397SGGray      (bool) True if space group is a gray group (incommensurate magnetic structures)
398SGInv       (bool) True if centrosymmetric, False if not
399SGLatt      (str)Lattice centering type. Will be one of
400            P, A, B, C, I, F, R
401SGLaue      (str) one of the following 14 Laue classes:
402            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
403            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m
404SGOps       (list) symmetry operations as a list of form
405            ``[[M1,T1], [M2,T2],...]``
406            where :math:`M_n` is a 3x3 np.array
407            and :math:`T_n` is a length 3 np.array.
408            Atom coordinates are transformed where the
409            Asymmetric unit coordinates [X is (x,y,z)]
410            are transformed using
411            :math:`X^\\prime = M_n*X+T_n`
412SGPolax     (str) Axes for space group polarity. Will be one of
413            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
414            'xyz'. In the case where axes are arbitrary
415            '111' is used (P 1, and ?).
416SGPtGrp     (str) Point group of the space group
417SGUniq      unique axis if monoclinic. Will be
418            a, b, or c for monoclinic space groups.
419            Will be blank for non-monoclinic.
420SGSpin      mag - (list) of spin flip operatiors (+1 or -1) for the space group operations
421SGSys       (str) symmetry unit cell: type one of
422            'triclinic', 'monoclinic', 'orthorhombic',
423            'tetragonal', 'rhombohedral', 'trigonal',
424            'hexagonal', 'cubic'
425SSGK1       (list) Superspace multipliers
426SpGrp       (str) space group symbol
427SpnFlp      mag - (list) Magnetic spin flips for every magnetic space group operator
428==========  ========================================================================================
429
430.. _SSGData_table:
431
432.. index::
433   single: Superspace Group Data description
434   single: Data object descriptions; Superspace Group Data
435
436Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
437and the information is placed in a SSGdata object
438which is a dict with these keys:
439
440.. tabularcolumns:: |l|p{4.5in}|
441
442==========  ====================================================
443  key         explanation
444==========  ====================================================
445SSGCen      (list) 4D cell centering vectors [0,0,0,0] at least
446SSGK1       (list) Superspace multipliers
447SSGOps      (list) 4D symmetry operations as [M,T] so that M*x+T = x'
448SSpGrp      (str) superspace group symbol extension to space group
449            symbol, accidental spaces removed
450modQ        (list) modulation/propagation vector
451modSymb     (list of str) Modulation symbols
452==========  ====================================================
453
454
455Phase Information
456--------------------
457
458.. index::
459   single: Phase information record description
460
461Phase information is placed in one of the following keys:
462
463.. tabularcolumns:: |l|p{4.5in}|
464
465==========  ==============================================================
466  key         explanation
467==========  ==============================================================
468General       Overall information about a phase
469Histograms    Information about each histogram linked to the
470              current phase as well as parameters that
471              are defined for each histogram and phase
472              (such as sample peak widths and preferred
473              orientation parameters.
474Atoms         Contains a list of atoms, as described in the
475              :ref:`Atom Records <Atoms_table>` description.
476Drawing       Parameters that determine how the phase is
477              displayed, including a list of atoms to be
478              included, as described in the
479              :ref:`Drawing Atom Records <Drawing_atoms_table>`
480              description
481MCSA          Monte-Carlo simulated annealing parameters
482pId           The index of each phase in the project, numbered
483              starting at 0
484ranId         An int value with a unique value for each phase
485RBModels      A list of dicts with parameters for each
486              rigid body inserted into the current phase,
487              as defined in the
488              :ref:`Rigid Body Insertions <Rigid_Body_Insertions>`.
489              Note that the rigid bodies are defined as
490              :ref:`Rigid Body Objects <RBData_table>`
491RMC           PDF modeling parameters
492Pawley ref    Pawley refinement parameters
493
494==========  ==============================================================
495
496.. _Atoms_table:
497
498.. index::
499   single: Atoms record description
500   single: Data object descriptions; Atoms record
501
502--------------------
503Atom Records
504--------------------
505
506If ``phasedict`` points to the phase information in the data tree, then
507atoms are contained in a list of atom records (list) in
508``phasedict['Atoms']``. Also needed to read atom information
509are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
510which define locations in the atom record, as shown below. Items shown are
511always present; additional ones for macromolecular phases are marked 'mm',
512and those for magnetic structures are marked 'mg'
513
514.. tabularcolumns:: |l|p{4.5in}|
515
516==============      ====================================================
517location            explanation
518==============      ====================================================
519ct-4                mm - (str) residue number
520ct-3                mm - (str) residue name (e.g. ALA)
521ct-2                mm - (str) chain label
522ct-1                (str) atom label
523ct                  (str) atom type
524ct+1                (str) refinement flags; combination of 'F', 'X', 'U', 'M'
525cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
526cx+3                (float) site occupancy
527cx+4,cx+5,cx+6      mg - (list) atom magnetic moment along a,b,c in Bohr magnetons
528cs                  (str) site symmetry
529cs+1                (int) site multiplicity
530cia                 (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
531cia+1               (float) Uiso
532cia+2...cia+7       (6 floats) U11, U22, U33, U12, U13, U23
533atom[cia+8]         (int) unique atom identifier
534
535==============      ====================================================
536
537.. _Drawing_atoms_table:
538
539.. index::
540   single: Drawing atoms record description
541   single: Data object descriptions; Drawing atoms record
542
543----------------------------
544Drawing Atom Records
545----------------------------
546
547If ``phasedict`` points to the phase information in the data tree, then
548drawing atoms are contained in a list of drawing atom records (list) in
549``phasedict['Drawing']['Atoms']``. Also needed to read atom information
550are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
551which define locations in the atom record, as shown below. Items shown are
552always present; additional ones for macromolecular phases are marked 'mm',
553and those for magnetic structures are marked 'mg'
554
555.. tabularcolumns:: |l|p{4.5in}|
556
557==============   ===================================================================================
558location            explanation
559==============   ===================================================================================
560ct-4                mm - (str) residue number
561ct-3                mm - (str) residue name (e.g. ALA)
562ct-2                mm - (str) chain label
563ct-1                (str) atom label
564ct                  (str) atom type
565cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
566cx+3,cx+4,cx+5      mg - (3 floats) atom magnetic moment along a,b,c in Bohr magnetons
567cs-1                (str) Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1')
568cs                  (str) atom drawing style; e.g. 'balls & sticks'
569cs+1                (str) atom label style (e.g. 'name')
570cs+2                (int) atom color (RBG triplet)
571cs+3                (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
572cs+4                (float) Uiso
573cs+5...cs+11        (6 floats) U11, U22, U33, U12, U13, U23
574ci                  (int) unique atom identifier; matches source atom Id in Atom Records
575==============   ===================================================================================
576
577.. _Rigid_Body_Insertions:
578
579----------------------------
580Rigid Body Insertions
581----------------------------
582
583If ``phasedict`` points to the phase information in the data tree, then
584rigid body information is contained in list(s) in
585``phasedict['RBModels']['Residue']`` and/or ``phasedict['RBModels']['Vector']``
586for each rigid body inserted into the current phase.
587
588.. tabularcolumns:: |l|p{4.5in}|
589
590==============   ===================================================================================
591key              explanation
592==============   ===================================================================================
593fixOrig           Should the origin be fixed (when editing, not the refinement flag)
594Ids               Ids for assignment of atoms in the rigid body
595numChain          Chain number for macromolecular fits
596Orient            Orientation of the RB as a quaternion and a refinement flag (' ', 'A' or 'AV')
597OrientVec         Orientation of the RB expressed as a vector and azimuthal rotation angle
598Orig              Origin of the RB in fractional coordinates and refinement flag (bool)
599RBId              References the unique ID of a rigid body in the
600                  :ref:`Rigid Body Objects <RBData_table>`
601RBname            The name for the rigid body (str)
602AtomFrac          The atom fractions for the rigid body
603ThermalMotion     The thermal motion description for the rigid body, which includes a choice for
604                  the model and can include TLS parameters or an overall Uiso value.
605Torsions          Defines the torsion angle and refinement flag for each torsion defined in
606                  the :ref:`Rigid Body Object <RBData_table>`
607==============   ===================================================================================
608
609.. _Powder_table:
610
611.. index::
612   single: Powder data object description
613   single: Data object descriptions; Powder Data
614
615Powder Diffraction Tree Items
616-----------------------------
617
618Every powder diffraction histogram is stored in the GSAS-II data tree
619with a top-level entry named beginning with the string "PWDR ". The
620diffraction data for that information are directly associated with
621that tree item and there are a series of children to that item. The
622routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
623and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
624load this information into a dictionary where the child tree name is
625used as a key, and the information in the main entry is assigned
626a key of ``Data``, as outlined below.
627
628.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
629
630======================     ===============  ===========================================================
631  key                       sub-key          explanation
632======================     ===============  ===========================================================
633Comments                    \\               (list of str) Text strings extracted from the original powder
634                                            data header. These cannot be changed by the user;
635                                            it may be empty.
636Limits                      \\               (list) two two element lists, as [[Ld,Hd],[L,H]]
637                                            where L and Ld are the current and default lowest
638                                            two-theta value to be used and
639                                            where H and Hd are the current and default highest
640                                            two-theta value to be used.
641Reflection Lists            \\               (dict of dicts) with an entry for each phase in the
642                                            histogram. The contents of each dict item
643                                            is a dict containing reflections, as described in
644                                            the :ref:`Powder Reflections <PowderRefl_table>`
645                                            description.
646Instrument Parameters       \\               (dict) The instrument parameters uses different dicts
647                                            for the constant wavelength (CW) and time-of-flight (TOF)
648                                            cases. See below for the descriptions of each.
649wtFactor                    \\               (float) A weighting factor to increase or decrease
650                                            the leverage of data in the histogram .
651                                            A value of 1.0 weights the data with their
652                                            standard uncertainties and a larger value
653                                            increases the weighting of the data (equivalent
654                                            to decreasing the uncertainties).
655Sample Parameters           \\               (dict) Parameters that describe how
656                                            the data were collected, as listed
657                                            below. Refinable parameters are a list containing
658                                            a float and a bool, where the second value
659                                            specifies if the value is refined, otherwise
660                                            the value is a float unless otherwise noted.
661\\                           Scale           The histogram scale factor (refinable)
662\\                           Absorption      The sample absorption coefficient as
663                                            :math:`\\mu r` where r is the radius
664                                            (refinable). Only valid for Debye-Scherrer geometry.
665\\                           SurfaceRoughA   Surface roughness parameter A as defined by
666                                            Surotti, *J. Appl. Cryst*, **5**, 325-331, 1972.
667                                            (refinable - only valid for Bragg-Brentano geometry)
668\\                           SurfaceRoughB   Surface roughness parameter B (refinable -
669                                            only valid for Bragg-Brentano geometry)
670\\                           DisplaceX,      Sample displacement from goniometer center
671                            DisplaceY       where Y is along the beam direction and
672                                            X is perpendicular. Units are :math:`\\mu m`
673                                            (refinable).
674\\                           Phi, Chi,       Goniometer sample setting angles, in degrees.
675                            Omega
676\\                           Gonio. radius   Radius of the diffractometer in mm
677\\                           InstrName       (str) A name for the instrument, used in preparing
678                                            a CIF .
679\\                           Force,          Variables that describe how the measurement
680                            Temperature,    was performed. Not used directly in
681                            Humidity,       any computations.
682                            Pressure,
683                            Voltage
684\\                           ranId           (int) The random-number Id for the histogram
685                                            (same value as where top-level key is ranId)
686\\                           Type            (str) Type of diffraction data, may be 'Debye-Scherrer'
687                                            or 'Bragg-Brentano' .
688hId                         \\               (int) The number assigned to the histogram when
689                                            the project is loaded or edited (can change)
690ranId                       \\               (int) A random number id for the histogram
691                                            that does not change
692Background                  \\               (list) The background is stored as a list with where
693                                            the first item in the list is list and the second
694                                            item is a dict. The list contains the background
695                                            function and its coefficients; the dict contains
696                                            Debye diffuse terms and background peaks.
697                                            (TODO: this needs to be expanded.)
698Data                        \\               (list) The data consist of a list of 6 np.arrays
699                                            containing in order:
700
701                                            0. the x-postions (two-theta in degrees),
702                                            1. the intensity values (Yobs),
703                                            2. the weights for each Yobs value
704                                            3. the computed intensity values (Ycalc)
705                                            4. the background values
706                                            5. Yobs-Ycalc
707======================     ===============  ===========================================================
708
709.. _CWPowder_table:
710
711.. index::
712   single: Powder data CW Instrument Parameters
713
714-----------------------------
715CW Instrument Parameters
716-----------------------------
717
718Instrument Parameters are placed in a list of two dicts,
719where the keys in the first dict are listed below. Note that the dict contents are different for
720constant wavelength (CW) vs. time-of-flight (TOF) histograms.
721The value for each item is a list containing three values: the initial value, the current value
722and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
723cannot be refined. The first and second values are floats unless otherwise noted.
724Items not refined are noted as [*]
725
726.. tabularcolumns:: |l|p{1in}|p{4in}|
727
728========================    ===============  ===========================================================
729  key                       sub-key           explanation
730========================    ===============  ===========================================================
731Instrument Parameters[0]    Type [*]            (str) Histogram type:
732                                                * 'PXC' for constant wavelength x-ray
733                                                * 'PNC' for constant wavelength neutron
734\\                           Bank [*]            (int) Data set number in a multidata file (usually 1)
735\\                           Lam                 (float) Specifies a wavelength in :math:`\\AA`
736\\                           Lam1 [*]            (float) Specifies the primary wavelength in
737                                                :math:`\\AA`, used in place of Lam
738                                                when an :math:`\\alpha_1, \\alpha_2`
739                                                source is used.
740\\                           Lam2 [*]            (float) Specifies the secondary wavelength in
741                                                :math:`\\AA`, used with Lam1
742\\                           I(L2)/I(L1)         (float) Ratio of Lam2 to Lam1, used with Lam1
743\\                           Zero                (float) Two-theta zero correction in *degrees*
744\\                           Azimuth [*]         (float) Azimuthal setting angle for data recorded with differing setting angles
745\\                           U, V, W             (float) Cagliotti profile coefficients
746                                                for Gaussian instrumental broadening, where the
747                                                FWHM goes as
748                                                :math:`U \\tan^2\\theta + V \\tan\\theta + W`
749\\                           X, Y, Z             (float) Cauchy (Lorentzian) instrumental broadening coefficients
750\\                           SH/L                (float) Variant of the Finger-Cox-Jephcoat asymmetric
751                                                peak broadening ratio. Note that this is the
752                                                sum of S/L and H/L where S is
753                                                sample height, H is the slit height and
754                                                L is the goniometer diameter.
755\\                           Polariz.            (float) Polarization coefficient.
756Instrument Parameters[1]                        (empty dict)
757========================    ===============  ===========================================================
758
759.. _TOFPowder_table:
760
761.. index::
762   single: Powder data TOF Instrument Parameters
763
764-----------------------------
765TOF Instrument Parameters
766-----------------------------
767
768Instrument Parameters are also placed in a list of two dicts,
769where the keys in each dict listed below, but here for
770time-of-flight (TOF) histograms.
771The value for each item is a list containing three values: the initial value, the current value
772and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
773cannot be refined. The first and second values are floats unless otherwise noted.
774Items not refined are noted as [*]
775
776.. tabularcolumns:: |l|p{1.5in}|p{4in}|
777
778========================    ===============  ===========================================================
779  key                        sub-key          explanation
780========================    ===============  ===========================================================
781Instrument Parameters[0]    Type [*]            (str) Histogram type:
782                                                * 'PNT' for time of flight neutron
783\\                           Bank                (int) Data set number in a multidata file
784\\                           2-theta [*]         (float) Nominal scattering angle for the detector
785\\                           fltPath [*]         (float) Total flight path source-sample-detector
786\\                           Azimuth [*]         (float) Azimuth angle for detector right hand rotation
787                                                from horizontal away from source
788\\                           difC,difA,          (float) Diffractometer constants for conversion of d-spacing to TOF
789                            difB                in microseconds
790\\                           Zero                (float) Zero point offset (microseconds)
791\\                           alpha               (float) Exponential rise profile coefficients
792\\                           beta-0              (float) Exponential decay profile coefficients
793                            beta-1
794                            beta-q
795\\                           sig-0               (float) Gaussian profile coefficients
796                            sig-1
797                            sig-2
798                            sig-q   
799\\                           X,Y,Z               (float) Lorentzian profile coefficients
800Instrument Parameters[1]    Pdabc               (list of 4 float lists) Originally created for use in gsas as optional tables
801                                                of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation
802                                                from the d-spacing and these tables. The d-true column is apparently unused.
803========================    ===============  ===========================================================
804
805
806.. _PowderRefl_table:
807
808.. index::
809   single: Powder reflection object description
810   single: Data object descriptions; Powder Reflections
811
812Powder Reflection Data Structure
813--------------------------------
814
815For every phase in a histogram, the ``Reflection Lists`` value is a dict
816one element of which is `'RefList'`, which is a np.array containing
817reflections. The columns in that array are documented below.
818
819==========  ====================================================
820  index         explanation
821==========  ====================================================
822 0,1,2          h,k,l (float)
823 3              (int) multiplicity
824 4              (float) d-space, :math:`\\AA`
825 5              (float) pos, two-theta
826 6              (float) sig, Gaussian width
827 7              (float) gam, Lorenzian width
828 8              (float) :math:`F_{obs}^2`
829 9              (float) :math:`F_{calc}^2`
830 10             (float) reflection phase, in degrees
831 11             (float) intensity correction for reflection, this times
832                :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
833 12             (float) Preferred orientation correction
834 13             (float) Transmission (absorption correction)
835 14             (float) Extinction correction
836==========  ====================================================
837
838.. _Xtal_table:
839
840.. index::
841   single: Single Crystal data object description
842   single: Data object descriptions; Single crystal data
843
844Single Crystal Tree Items
845-------------------------
846
847Every single crystal diffraction histogram is stored in the GSAS-II data tree
848with a top-level entry named beginning with the string "HKLF ". The
849diffraction data for that information are directly associated with
850that tree item and there are a series of children to that item. The
851routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
852and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
853load this information into a dictionary where the child tree name is
854used as a key, and the information in the main entry is assigned
855a key of ``Data``, as outlined below.
856
857.. tabularcolumns:: |l|l|p{4in}|
858
859======================  ===============     ====================================================
860  key                      sub-key          explanation
861======================  ===============     ====================================================
862Data                        \\               (dict) that contains the
863                                            reflection table,
864                                            as described in the
865                                            :ref:`Single Crystal Reflections
866                                            <XtalRefl_table>`
867                                            description.
868
869Instrument Parameters       \\               (list) containing two dicts where the possible
870                                            keys in each dict are listed below. The value
871                                            for most items is a list containing two values:
872                                            the initial value, the current value.
873                                            The first and second
874                                            values are floats unless otherwise noted.
875\\                           Lam             (two floats) Specifies a wavelength in :math:`\\AA`
876\\                           Type            (two str values) Histogram type :
877                                            * 'SXC' for constant wavelength x-ray
878                                            * 'SNC' for constant wavelength neutron
879                                            * 'SNT' for time of flight neutron
880\\                           InstrName       (str) A name for the instrument, used in preparing a CIF
881wtFactor                    \\               (float) A weighting factor to increase or decrease
882                                            the leverage of data in the histogram.
883                                            A value of 1.0 weights the data with their
884                                            standard uncertainties and a larger value
885                                            increases the weighting of the data (equivalent
886                                            to decreasing the uncertainties).
887
888hId                         \\               (int) The number assigned to the histogram when
889                                            the project is loaded or edited (can change)
890ranId                       \\               (int) A random number id for the histogram
891                                            that does not change
892======================  ===============     ====================================================
893
894.. _XtalRefl_table:
895
896.. index::
897   single: Single Crystal reflection object description
898   single: Data object descriptions; Single Crystal Reflections
899
900Single Crystal Reflection Data Structure
901----------------------------------------
902
903For every single crystal a histogram, the ``'Data'`` item contains
904the structure factors as an np.array in item `'RefList'`.
905The columns in that array are documented below.
906
907.. tabularcolumns:: |l|p{4in}|
908
909==========  ====================================================
910  index         explanation
911==========  ====================================================
912 0,1,2          (float) h,k,l
913 3              (int) multiplicity
914 4              (float) d-space, :math:`\\AA`
915 5              (float) :math:`F_{obs}^2`
916 6              (float) :math:`\\sigma(F_{obs}^2)`
917 7              (float) :math:`F_{calc}^2`
918 8              (float) :math:`F_{obs}^2T`
919 9              (float) :math:`F_{calc}^2T`
920 10             (float) reflection phase, in degrees
921 11             (float) intensity correction for reflection, this times
922                :math:`F_{obs}^2` or :math:`F_{calc}^2`
923                gives Iobs or Icalc
924==========  ====================================================
925
926.. _Image_table:
927
928.. index::
929   image: Image data object description
930   image: Image object descriptions
931
932Image Data Structure
933--------------------
934
935Every 2-dimensional image is stored in the GSAS-II data tree
936with a top-level entry named beginning with the string "IMG ". The
937image data are directly associated with that tree item and there
938are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
939and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
940load this information into a dictionary where the child tree name is
941used as a key, and the information in the main entry is assigned
942a key of ``Data``, as outlined below.
943
944.. tabularcolumns:: |l|l|p{4in}|
945
946======================  ======================  ====================================================
947  key                      sub-key              explanation
948======================  ======================  ====================================================
949Comments                    \\                   (list of str) Text strings extracted from the original image data
950                                                header or a metafile. These cannot be changed by
951                                                the user; it may be empty.
952Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
953                                                value. Accomodates
954                                                detector orientations other than with the detector
955                                                X-axis
956                                                horizontal.
957\\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
958                                                during image integration multiplied by value. It must have the same size/shape as
959                                                the integrated image. NB: value < 0 for subtraction.
960\\                           calibrant           (str) The material used for determining the position/orientation
961                                                of the image. The data is obtained from :func:`ImageCalibrants`
962                                                and UserCalibrants.py (supplied by user).
963\\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
964\\                           calibskip           (int) The number of expected diffraction lines skipped during the last
965                                                calibration run.
966\\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
967                                                strikes the detector plane as determined by calibration. This point
968                                                does not have to be within the limits of the detector boundaries.
969\\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
970                                                of the image is at the center line otherwise it is at the leading edge.
971\\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
972\\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
973                                                calibration calculations. See pixLimit for details as how point is found.
974\\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
975                                                ring offset at higher angles. Optionally determined by calibration.
976\\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
977\\                           distance            (float) The distance (mm) from sample to detector plane.
978\\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
979                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
980                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
981                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
982                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
983\\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
984\\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
985\\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
986                                                Required for texture calculations.
987\\                           invert_x            (bool) If True display the image with the x-axis inverted.
988\\                           invert_y            (bool) If True display the image with the y-axis inverted.
989\\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
990\\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
991\\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
992                                                intensities obtained during integration.
993\\                           outAzimuths         (int) The number of azimuth pie slices.
994\\                           outChannels         (int) The number of 2-theta steps.
995\\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
996\\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
997                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
998                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
999                                                Locations are used to construct rings of points for calibration calcualtions.
1000\\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
1001                                                integration using value.
1002\\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
1003                                                diffraction ring with the same d-spacing (dsp)
1004\\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
1005                                                selected by the user,
1006\\                           Range               (list) The minimum & maximum values of the image
1007\\                           rotation            (float) The angle between the x-axis and the vector about which the
1008                                                detector is tilted. Constrained to -180 to 180 deg.
1009\\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
1010                                                calculations.
1011\\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
1012                                                to cause correction to be applied.
1013\\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
1014\\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
1015\\                           showLines           (bool) If True then isplay the integration limits to be used.
1016\\                           size                (list:int) The number of pixels on the image x & y axes
1017\\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
1018\\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
1019\\                           wavelength          (float) The radiation wavelength (:math:`\\AA`) as entered by the user
1020                                                (or someday obtained from the image header).
1021Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
1022                                                to be excluded from integration
1023\\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
1024                                                of which is excluded from recalibration and integration. Only one frame is allowed.
1025\\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
1026                                                from integration.
1027\\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
1028                                                to be excluded from integration.
1029\\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
1030                                                to be excluded from integration.
1031\\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
1032                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
1033\\                           SpotMask            (dict: int & array)
1034                                                'esdMul'(int) number of standard deviations above mean ring intensity to mask
1035                                                'spotMask' (bool array) the spot mask for every pixel in image         
1036
1037Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
1038\\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
1039                                                These will be restricted by space group symmetry; result of strain fit refinement.
1040\\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
1041\\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
1042                                                and are used to determine the strain tensor.
1043                                                The dictionary items are:
1044                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
1045                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
1046                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
1047                                                'Esig': (list: float) Esds for Emat from fitting.
1048                                                'pixLimit': (int) Search range to find highest point on ring for each data point
1049                                                'cutoff': (float) I/Ib cutoff for searching.
1050                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
1051                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
1052                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
1053
1054======================  ======================  ====================================================
1055
1056.. _parmDict_table:
1057
1058.. index::
1059   single: Parameter dictionary
1060
1061Parameter Dictionary
1062-------------------------
1063
1064The parameter dictionary contains all of the variable parameters for the refinement.
1065The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
1066It is prepared in two ways. When loaded from the tree
1067(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
1068:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
1069the values are lists with two elements: ``[value, refine flag]``
1070
1071When loaded from the GPX file (in
1072:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
1073dict is the actual parameter value (usually a float, but sometimes a
1074letter or string flag value (such as I or A for iso/anisotropic).
1075
1076Texture implementation
1077------------------------------
1078
1079There are two different places where texture can be treated in GSAS-II.
1080One is for mitigating the effects of texture in a structural refinement.
1081The other is for texture characterization.
1082
1083For reducing the effect of texture in a structural refinement
1084there are entries labeled preferred orientation in each phase's
1085data tab. Two different approaches can be used for this, the March-Dollase
1086model and spherical harmonics.
1087
1088For the March-Dollase model, one axis in reciprocal space is designated as
1089unique (defaulting to the 001 axis) and reflections are corrected
1090according to the angle they make with this axis depending on
1091the March-Dollase ratio. (If unity, no correction is made).
1092The ratio can be greater than one or less than one depending on if
1093crystallites oriented along the designated axis are
1094overrepresented or underrepresented. For most crystal systems there is an
1095obvious choice for the direction of the unique axis and then only a single
1096term needs to be refined. If the number is close to 1, then the correction
1097is not needed.
1098
1099The second method for reducing the effect of texture in a structural
1100refinement is to create a crystallite orientation probability surface as an
1101expansion in terms spherical harmonic functions. Only functions consistent with
1102cylindrical diffraction suymmetry and having texture symmetry
1103consistent with the Laue class of phase are used and are allowed,
1104so the higher the symmetry the fewer terms that are available for a given spherical harmonics order.
1105To use this correction, select the lowest order that provides
1106refinable terms and perform a refinement. If the texture index remains close to
1107one, then the correction is not needed. If a significant improvement is
1108noted in the profile Rwp, one may wish to see if a higher order expansion
1109gives an even larger improvement.
1110
1111To characterize texture in a material, generally one needs data collected with the
1112sample at multiple orientations or, for TOF, with detectors at multiple
1113locations around the sample. In this case the detector orientation is given in
1114each histogram's Sample Parameters and the sample's orientation is described
1115with the Euler angles specifed on the phase's Texture tab, which is also
1116where the texture type (cylindrical, rolling,...) and the spherical
1117harmonic order is selected. This should not be used with a single dataset and
1118should not be used if the preferred orientations corrections are used.
1119
1120The coordinate system used for texture characterization is defined where
1121the sample coordinates (Psi, gamma) are defined with an instrument coordinate
1122system (I, J, K) such that K is normal to the diffraction plane and J is coincident with the
1123direction of the incident radiation beam toward the source. We further define
1124a standard set of right-handed goniometer eulerian angles (Omega, Chi, Phi) so that Omega and Phi are
1125rotations about K and Chi is a rotation about J when Omega = 0. Finally, as the sample
1126may be mounted so that the sample coordinate system (Is, Js, Ks) does not coincide with
1127the instrument coordinate system (I, J, K), we define three eulerian sample rotation angles
1128(Omega-s, Chi-s, Phi-s) that describe the rotation from (Is, Js, Ks) to (I, J, K). The sample rotation
1129angles are defined so that with the goniometer angles at zero Omega-s and Phi-s are rotations
1130about K and Chi-s is a rotation about J.
1131
1132Three typical examples:
1133    1) Bragg-Brentano laboratory diffractometer: Chi=0
1134    2) Debye-Scherrer counter detector; sample capillary axis perpendicular to diffraction plane: Chi=90
1135    3) Debye-Scherrer 2D area detector positioned directly behind sample; sample capillary axis horizontal; Chi=0
1136            NB: The area detector azimuthal angle = 0 in horizontal plane to right as viewed from x-ray source & 90 at vertical "up" direction
1137           
1138ISODISTORT implementation
1139------------------------------
1140
1141CIFs prepared with the ISODISTORT web site
1142https://stokes.byu.edu/iso/isodistort_version5.6.1/isodistort.php
1143[B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions."
1144 J. Appl. Cryst. 39, 607-614 (2006).] can be read into GSAS-II using import CIF. This will cause constraints to be established for
1145structural distortion modes read from the CIF. At present, of the five types of modes  only displacive(``_iso_displacivemode``...)
1146and occupancy (``_iso_occupancymode``...) are processed. Not yet processed: ``_iso_magneticmode``...,
1147``_iso_rotationalmode``... & ``_iso_strainmode``...
1148
1149The CIF importer :mod:`G2phase_CIF` implements class :class:`G2phase_CIF.CIFPhaseReader` which offers two methods associated
1150with ISODISTORT (ID) input. Method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_test` checks to see if a CIF block contains
1151the loops with ``_iso_displacivemode_label`` or  ``_iso_occupancymode_label`` items. If so, method
1152:meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_proc` is called to read and interpret them. The results are placed into the
1153reader object's ``.Phase`` class variable as a dict item with key ``'ISODISTORT'``.
1154
1155Note 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
1156:func:`G2phase_CIF.ISODISTORT_shortLbl` is used to create a short name for this, such as R5_T1u(a) which is made unique
1157by addition of _n if the short name is duplicated. As each mode is processed, a constraint corresponding to that mode is
1158created and is added to list in the reader object's ``.Constraints`` class variable. Items placed into that list can either
1159be a list, which corresponds to a function (new var) type :ref:`constraint definition <Constraints_table>` entry, or an item
1160can be a dict, which provides help information for each constraint.
1161
1162------------------------------
1163Displacive modes
1164------------------------------
1165
1166The coordinate variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoVarList']`` and the
1167corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2VarList']``.
1168The mode variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoModeList']`` and the
1169corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2ModeList']``.
1170[Use ``str(G2VarObj)`` to get the variable name from the G2VarObj object, but note that the phase number, *n*, for the prefix
1171 "*n*::" cannot be determined as the phase number is not yet assigned.]
1172
1173Displacive modes are a bit complex in that they relate to delta displacements, relative to an offset value for each coordinate,
1174and because the modes are normalized, while GSAS-II also uses displacements, but these are added to the coordinates after
1175each refinement cycle and the delta values are set to zero. ISODISTORT uses fixed offsets (subtracted from the actual position
1176to obtain the delta values) that are taken from ``_iso_coordinate_formula`` and these are placed in
1177``.Phase['ISODISTORT']['ParentStructure]`` (keyed by atom label). The normalization factors (which the delta values are divided by)
1178are taken from ``_iso_displacivemodenorm_value`` and are placed in ``.Phase['ISODISTORT']['NormList']`` in the same order as as
1179``...['IsoModeList']`` and ``...['G2ModeList']``.
1180
1181The CIF contains a sparse matrix, from the ``loop_`` containing ``_iso_displacivemodematrix_value`` which provides the equations
1182for determining the mode values from the coordinates, that matrix is placed in ``.Phase['ISODISTORT']['Mode2VarMatrix']``.
1183The matrix is inverted to produce ``.Phase['ISODISTORT']['Var2ModeMatrix']``, which determines how to compute the
1184mode values from the delta coordinate values. These values are used for the in :func:`GSASIIconstrGUI.ShowIsoDistortCalc`
1185which shows coordinate and mode values, the latter with s.u. values.
1186
1187
1188------------------------------
1189Occupancy modes
1190------------------------------
1191
1192
1193The delta occupancy variables, as named by ISODISTORT, are placed in
1194``.Phase['ISODISTORT']['OccVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed
1195in ``.Phase['ISODISTORT']['G2OccVarList']``. The mode variables, as named by ISODISTORT, are placed in
1196``.Phase['ISODISTORT']['OccModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed
1197in ``.Phase['ISODISTORT']['G2OccModeList']``.
1198
1199Occupancy modes, like Displacive modes, are also refined as delta values.  However, GSAS-II directly refines the fractional
1200occupancies. Offset values for each atom, are taken from ``_iso_occupancy_formula`` and are placed in
1201``.Phase['ISODISTORT']['ParentOcc]``. (Offset values are subtracted from the actual position to obtain the delta values.)
1202Modes are normalized (where the mode values are divided by the normalization factor) are taken from ``_iso_occupancymodenorm_value``
1203and are placed in ``.Phase['ISODISTORT']['OccNormList']`` in the same order as as ``...['OccModeList']`` and
1204``...['G2OccModeList']``.
1205
1206The CIF contains a sparse matrix, from the ``loop_`` containing ``_iso_occupancymodematrix_value``, which provides the
1207equations for determining the mode values from the coordinates. That matrix is placed in ``.Phase['ISODISTORT']['Occ2VarMatrix']``.
1208The matrix is inverted to produce ``.Phase['ISODISTORT']['Var2OccMatrix']``, which determines how to compute the
1209mode values from the delta coordinate values.
1210
1211
1212------------------------------
1213Mode Computations
1214------------------------------
1215
1216Constraints are processed after the CIF has been read in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` or 
1217:meth:`GSASIIscriptable.G2Project.add_phase` by moving them from the reader object's ``.Constraints``
1218class variable to the Constraints tree entry's ['Phase'] list (for list items defining constraints) or
1219the Constraints tree entry's ['_Explain'] dict (for dict items defining constraint help information)
1220
1221The information in ``.Phase['ISODISTORT']`` is used in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1222values, the latter with s.u. values. This can be called from the Constraints and Phase/Atoms tree items.
1223
1224Before each refinement, constraints are processed as :ref:`described elsewhere <Constraints_processing>`. After a refinement
1225is complete, :func:`GSASIImapvars.PrintIndependentVars` shows the shifts and s.u.'s on the refined modes,
1226using GSAS-II values, but :func:`GSASIIstrIO.PrintISOmodes` prints the ISODISTORT modes as computed in the web site.
1227
1228
1229.. _ParameterLimits:
1230
1231.. index::
1232   single: Parameter limits
1233
1234Parameter Limits
1235------------------------------
1236
1237One of the most often requested "enhancements" for GSAS-II would be the inclusion
1238of constraints to force parameters such as occupancies or Uiso values to stay within
1239expected ranges. While it is possible for users to supply their own restraints that would
1240perform this by supplying an appropriate expression with the "General" restraints, the
1241GSAS-II authors do not feel that use of restraints or constraints are a good solution for
1242this common problem where parameters refine to non-physical values. This is because when
1243this occurs, most likely one of the following cases is occurring:
1244
1245#. there is a significant problem
1246   with the model, for example for an x-ray fit if an O atom is placed where a S is actually
1247   present, the Uiso will refine artificially small or the occupancy much larger than unity
1248   to try to compensate for the missing electrons; or
1249 
1250#. the data are simply insensitive
1251   to the parameter or combination of parameters, for example unless very high-Q data
1252   are included, the effects of a occupancy and Uiso value can have compensating effects,
1253   so an assumption must be made; likewise, with neutron data natural-abundance V atoms
1254   are nearly invisible due to weak coherent scattering. No parameters can be fit for a
1255   V atom with neutrons.
1256
1257#. the parameter is non-physical (such as a negative Uiso value) but within
1258   two sigma (sigma = standard uncertainty, aka e.s.d.) of a reasonable value,
1259   in which case the
1260   value is not problematic as it is experimentally indistinguishable from an
1261   expected value. 
1262
1263#. there is a systematic problem with the data (experimental error)
1264
1265In all these cases, this situation needs to be reviewed by a crystallographer to decide
1266how to best determine a structural model for these data. An implementation with a constraint
1267or restraint is likely to simply hide the problem from the user, making it more probable
1268that a poor model choice is obtained.
1269
1270What GSAS-II does implement is to allow users to specify ranges for parameters
1271that works by disabling
1272refinement of parameters that refine beyond either a lower limit or an upper limit, where
1273either or both may be optionally specified. Parameters limits are specified in the Controls
1274tree entry in dicts named as ``Controls['parmMaxDict']`` and ``Controls['parmMinDict']``, where
1275the keys are :class:`G2VarObj` objects corresponding to standard GSAS-II variable
1276(see :func:`getVarDescr` and :func:`CompileVarDesc`) names, where a
1277wildcard ('*') may optionally be used for histogram number or atom number
1278(phase number is intentionally not  allowed as a wildcard as it makes little sense
1279to group the same parameter together different phases). Note
1280that :func:`prmLookup` is used to see if a name matches a wildcard. The upper or lower limit
1281is placed into these dicts as a float value. These values can be edited using the window
1282created by the Calculate/"View LS parms" menu command or in scripting with the
1283:meth:`GSASIIscriptable.G2Project.set_Controls` function.
1284In the GUI, a checkbox labeled "match all histograms/atoms" is used to insert a wildcard
1285into the appropriate part of the variable name.
1286
1287When a refinement is conducted, routine :func:`GSASIIstrMain.dropOOBvars` is used to
1288find parameters that have refined to values outside their limits. If this occurs, the parameter
1289is set to the limiting value and the variable name is added to a list of frozen variables
1290(as a :class:`G2VarObj` objects) kept in a list in the
1291``Controls['parmFrozen']`` dict. In a sequential refinement, this is kept separate for
1292each histogram as a list in
1293``Controls['parmFrozen'][histogram]`` (where the key is the histogram name) or as a list in
1294``Controls['parmFrozen']['FrozenList']`` for a non-sequential fit.
1295This allows different variables
1296to be frozen in each section of a sequential fit.
1297Frozen parameters are not included in refinements through removal from the
1298list of parameters to be refined (``varyList``) in :func:`GSASIIstrMain.Refine` or
1299:func:`GSASIIstrMain.SeqRefine`.
1300The data window for the Controls tree item shows the number of Frozen variables and
1301the individual variables can be viewed with the Calculate/"View LS parms" menu window or
1302obtained with :meth:`GSASIIscriptable.G2Project.get_Frozen`.
1303Once a variable is frozen, it will not be refined in any
1304future refinements unless the the variable is removed (manually) from the list. This can also
1305be done with the Calculate/"View LS parms" menu window or
1306:meth:`GSASIIscriptable.G2Project.set_Frozen`.
1307
1308
1309.. seealso::
1310  :class:`G2VarObj`
1311  :func:`getVarDescr`
1312  :func:`CompileVarDesc`
1313  :func:`prmLookup`
1314  :class:`GSASIIctrlGUI.ShowLSParms`
1315  :class:`GSASIIctrlGUI.VirtualVarBox`
1316  :func:`GSASIIstrIO.SetUsedHistogramsAndPhases`
1317  :func:`GSASIIstrIO.SaveUpdatedHistogramsAndPhases`
1318  :func:`GSASIIstrIO.SetSeqResult`
1319  :func:`GSASIIstrMain.dropOOBvars`
1320  :meth:`GSASIIscriptable.G2Project.set_Controls`
1321  :meth:`GSASIIscriptable.G2Project.get_Frozen`
1322  :meth:`GSASIIscriptable.G2Project.set_Frozen`
1323
1324*Classes and routines*
1325----------------------
1326
1327'''
1328from __future__ import division, print_function
1329import platform
1330import re
1331import random as ran
1332import sys
1333import os.path as ospath
1334if '2' in platform.python_version_tuple()[0]:
1335    import cPickle
1336else:
1337    import pickle as cPickle
1338import GSASIIpath
1339import GSASIImath as G2mth
1340import GSASIIspc as G2spc
1341import numpy as np
1342
1343GSASIIpath.SetVersionNumber("$Revision: 5041 $")
1344
1345DefaultControls = {
1346    'deriv type':'analytic Hessian',
1347    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
1348    'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
1349    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
1350    'Author':'no name','newLeBail':False,
1351    'FreePrm1':'Sample humidity (%)',
1352    'FreePrm2':'Sample voltage (V)',
1353    'FreePrm3':'Applied load (MN)',
1354    'ShowCell':False,
1355    }
1356'''Values to be used as defaults for the initial contents of the ``Controls``
1357data tree item.
1358'''
1359def StripUnicode(string,subs='.'):
1360    '''Strip non-ASCII characters from strings
1361
1362    :param str string: string to strip Unicode characters from
1363    :param str subs: character(s) to place into string in place of each
1364      Unicode character. Defaults to '.'
1365
1366    :returns: a new string with only ASCII characters
1367    '''
1368    s = ''
1369    for c in string:
1370        if ord(c) < 128:
1371            s += c
1372        else:
1373            s += subs
1374    return s
1375#    return s.encode('ascii','replace')
1376
1377def MakeUniqueLabel(lbl,labellist):
1378    '''Make sure that every a label is unique against a list by adding
1379    digits at the end until it is not found in list.
1380
1381    :param str lbl: the input label
1382    :param list labellist: the labels that have already been encountered
1383    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
1384      ``_10-99``, etc.) appended at the end
1385    '''
1386    lbl = StripUnicode(lbl.strip(),'_')
1387    if not lbl: # deal with a blank label
1388        lbl = '_1'
1389    if lbl not in labellist:
1390        labellist.append(lbl)
1391        return lbl
1392    i = 1
1393    prefix = lbl
1394    if '_' in lbl:
1395        prefix = lbl[:lbl.rfind('_')]
1396        suffix = lbl[lbl.rfind('_')+1:]
1397        try:
1398            i = int(suffix)+1
1399        except: # suffix could not be parsed
1400            i = 1
1401            prefix = lbl
1402    while prefix+'_'+str(i) in labellist:
1403        i += 1
1404    else:
1405        lbl = prefix+'_'+str(i)
1406        labellist.append(lbl)
1407    return lbl
1408
1409PhaseIdLookup = {}
1410'''dict listing phase name and random Id keyed by sequential phase index as a str;
1411best to access this using :func:`LookupPhaseName`
1412'''
1413PhaseRanIdLookup = {}
1414'''dict listing phase sequential index keyed by phase random Id;
1415best to access this using :func:`LookupPhaseId`
1416'''
1417HistIdLookup = {}
1418'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
1419best to access this using :func:`LookupHistName`
1420'''
1421HistRanIdLookup = {}
1422'''dict listing histogram sequential index keyed by histogram random Id;
1423best to access this using :func:`LookupHistId`
1424'''
1425AtomIdLookup = {}
1426'''dict listing for each phase index as a str, the atom label and atom random Id,
1427keyed by atom sequential index as a str;
1428best to access this using :func:`LookupAtomLabel`
1429'''
1430AtomRanIdLookup = {}
1431'''dict listing for each phase the atom sequential index keyed by atom random Id;
1432best to access this using :func:`LookupAtomId`
1433'''
1434ShortPhaseNames = {}
1435'''a dict containing a possibly shortened and when non-unique numbered
1436version of the phase name. Keyed by the phase sequential index.
1437'''
1438ShortHistNames = {}
1439'''a dict containing a possibly shortened and when non-unique numbered
1440version of the histogram name. Keyed by the histogram sequential index.
1441'''
1442
1443#VarDesc = {}  # removed 1/30/19 BHT as no longer needed (I think)
1444#''' This dictionary lists descriptions for GSAS-II variables,
1445#as set in :func:`CompileVarDesc`. See that function for a description
1446#for how keys and values are written.
1447#'''
1448
1449reVarDesc = {}
1450''' This dictionary lists descriptions for GSAS-II variables where
1451keys are compiled regular expressions that will match the name portion
1452of a parameter name. Initialized in :func:`CompileVarDesc`.
1453'''
1454
1455reVarStep = {}
1456''' This dictionary lists the preferred step size for numerical
1457derivative computation w/r to a GSAS-II variable. Keys are compiled
1458regular expressions and values are the step size for that parameter.
1459Initialized in :func:`CompileVarDesc`.
1460'''
1461# create a default space group object for P1; N.B. fails when building documentation
1462try:
1463    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1464except:
1465    pass
1466
1467def GetPhaseNames(fl):
1468    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1469    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1470
1471    :param file fl: opened .gpx file
1472    :return: list of phase names
1473    '''
1474    PhaseNames = []
1475    while True:
1476        try:
1477            data = cPickle.load(fl)
1478        except EOFError:
1479            break
1480        datum = data[0]
1481        if 'Phases' == datum[0]:
1482            for datus in data[1:]:
1483                PhaseNames.append(datus[0])
1484    fl.seek(0)          #reposition file
1485    return PhaseNames
1486
1487def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1488    '''Create a new phase dict with default values for various parameters
1489
1490    :param str Name: Name for new Phase
1491
1492    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1493      defaults to data for P 1
1494
1495    :param list cell: unit cell parameter list; defaults to
1496      [1.0,1.0,1.0,90.,90,90.,1.]
1497
1498    '''
1499    if SGData is None: SGData = P1SGData
1500    if cell is None: cell=[1.0,1.0,1.0,90.,90.,90.,1.]
1501    phaseData = {
1502        'ranId':ran.randint(0,sys.maxsize),
1503        'General':{
1504            'Name':Name,
1505            'Type':'nuclear',
1506            'Modulated':False,
1507            'AtomPtrs':[3,1,7,9],
1508            'SGData':SGData,
1509            'Cell':[False,]+cell,
1510            'Pawley dmin':1.0,
1511            'Data plot type':'None',
1512            'SH Texture':{
1513                'Order':0,
1514                'Model':'cylindrical',
1515                'Sample omega':[False,0.0],
1516                'Sample chi':[False,0.0],
1517                'Sample phi':[False,0.0],
1518                'SH Coeff':[False,{}],
1519                'SHShow':False,
1520                'PFhkl':[0,0,1],
1521                'PFxyz':[0,0,1],
1522                'PlotType':'Pole figure',
1523                'Penalty':[['',],0.1,False,1.0]}},
1524        'Atoms':[],
1525        'Drawing':{},
1526        'Histograms':{},
1527        'Pawley ref':[],
1528        'RBModels':{},
1529        }
1530    if Super and Super.get('Use',False):
1531        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1532        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])[1]
1533        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1534
1535    return phaseData
1536
1537def ReadCIF(URLorFile):
1538    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1539    (from James Hester).
1540    The open routine gets confused with DOS names that begin with a letter and colon
1541    "C:\\dir\" so this routine will try to open the passed name as a file and if that
1542    fails, try it as a URL
1543
1544    :param str URLorFile: string containing a URL or a file name. Code will try first
1545      to open it as a file and then as a URL.
1546
1547    :returns: a PyCifRW CIF object.
1548    '''
1549    import CifFile as cif # PyCifRW from James Hester
1550
1551    # alternate approach:
1552    #import urllib
1553    #ciffile = 'file:'+urllib.pathname2url(filename)
1554
1555    try:
1556        fp = open(URLorFile,'r')
1557        cf = cif.ReadCif(fp)
1558        fp.close()
1559        return cf
1560    except IOError:
1561        return cif.ReadCif(URLorFile)
1562
1563def TestIndexAll():
1564    '''Test if :func:`IndexAllIds` has been called to index all phases and
1565    histograms (this is needed before :func:`G2VarObj` can be used.
1566
1567    :returns: Returns True if indexing is needed.
1568    '''
1569    if PhaseIdLookup or AtomIdLookup or HistIdLookup:
1570        return False
1571    return True
1572       
1573def IndexAllIds(Histograms,Phases):
1574    '''Scan through the used phases & histograms and create an index
1575    to the random numbers of phases, histograms and atoms. While doing this,
1576    confirm that assigned random numbers are unique -- just in case lightning
1577    strikes twice in the same place.
1578
1579    Note: this code assumes that the atom random Id (ranId) is the last
1580    element each atom record.
1581
1582    This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
1583    (which loads the histograms and phases from a GPX file),
1584    :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
1585    (which loads the histograms and phases from the data tree.) and
1586    :meth:`GSASIIconstrGUI.UpdateConstraints`
1587    (which displays & edits the constraints in a GUI)
1588
1589    TODO: do we need a lookup for rigid body variables?
1590    '''
1591    # process phases and atoms
1592    PhaseIdLookup.clear()
1593    PhaseRanIdLookup.clear()
1594    AtomIdLookup.clear()
1595    AtomRanIdLookup.clear()
1596    ShortPhaseNames.clear()
1597    for ph in Phases:
1598        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1599        ranId = Phases[ph]['ranId']
1600        while ranId in PhaseRanIdLookup:
1601            # Found duplicate random Id! note and reassign
1602            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1603            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1604        pId = str(Phases[ph]['pId'])
1605        PhaseIdLookup[pId] = (ph,ranId)
1606        PhaseRanIdLookup[ranId] = pId
1607        shortname = ph  #[:10]
1608        while shortname in ShortPhaseNames.values():
1609            shortname = ph[:8] + ' ('+ pId + ')'
1610        ShortPhaseNames[pId] = shortname
1611        AtomIdLookup[pId] = {}
1612        AtomRanIdLookup[pId] = {}
1613        for iatm,at in enumerate(Phases[ph]['Atoms']):
1614            ranId = at[cia+8]
1615            while ranId in AtomRanIdLookup[pId]: # check for dups
1616                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1617                at[cia+8] = ranId = ran.randint(0,sys.maxsize)
1618            AtomRanIdLookup[pId][ranId] = str(iatm)
1619            if Phases[ph]['General']['Type'] == 'macromolecular':
1620                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1621            else:
1622                label = at[ct-1]
1623            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1624    # process histograms
1625    HistIdLookup.clear()
1626    HistRanIdLookup.clear()
1627    ShortHistNames.clear()
1628    for hist in Histograms:
1629        ranId = Histograms[hist]['ranId']
1630        while ranId in HistRanIdLookup:
1631            # Found duplicate random Id! note and reassign
1632            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1633            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1634        hId = str(Histograms[hist]['hId'])
1635        HistIdLookup[hId] = (hist,ranId)
1636        HistRanIdLookup[ranId] = hId
1637        shortname = hist[:15]
1638        while shortname in ShortHistNames.values():
1639            shortname = hist[:11] + ' ('+ hId + ')'
1640        ShortHistNames[hId] = shortname
1641
1642def LookupAtomId(pId,ranId):
1643    '''Get the atom number from a phase and atom random Id
1644
1645    :param int/str pId: the sequential number of the phase
1646    :param int ranId: the random Id assigned to an atom
1647
1648    :returns: the index number of the atom (str)
1649    '''
1650    if not AtomRanIdLookup:
1651        raise Exception('Error: LookupAtomId called before IndexAllIds was run')
1652    if pId is None or pId == '':
1653        raise KeyError('Error: phase is invalid (None or blank)')
1654    pId = str(pId)
1655    if pId not in AtomRanIdLookup:
1656        raise KeyError('Error: LookupAtomId does not have phase '+pId)
1657    if ranId not in AtomRanIdLookup[pId]:
1658        raise KeyError('Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']')
1659    return AtomRanIdLookup[pId][ranId]
1660
1661def LookupAtomLabel(pId,index):
1662    '''Get the atom label from a phase and atom index number
1663
1664    :param int/str pId: the sequential number of the phase
1665    :param int index: the index of the atom in the list of atoms
1666
1667    :returns: the label for the atom (str) and the random Id of the atom (int)
1668    '''
1669    if not AtomIdLookup:
1670        raise Exception('Error: LookupAtomLabel called before IndexAllIds was run')
1671    if pId is None or pId == '':
1672        raise KeyError('Error: phase is invalid (None or blank)')
1673    pId = str(pId)
1674    if pId not in AtomIdLookup:
1675        raise KeyError('Error: LookupAtomLabel does not have phase '+pId)
1676    if index not in AtomIdLookup[pId]:
1677        raise KeyError('Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']')
1678    return AtomIdLookup[pId][index]
1679
1680def LookupPhaseId(ranId):
1681    '''Get the phase number and name from a phase random Id
1682
1683    :param int ranId: the random Id assigned to a phase
1684    :returns: the sequential Id (pId) number for the phase (str)
1685    '''
1686    if not PhaseRanIdLookup:
1687        raise Exception('Error: LookupPhaseId called before IndexAllIds was run')
1688    if ranId not in PhaseRanIdLookup:
1689        raise KeyError('Error: LookupPhaseId does not have ranId '+str(ranId))
1690    return PhaseRanIdLookup[ranId]
1691
1692def LookupPhaseName(pId):
1693    '''Get the phase number and name from a phase Id
1694
1695    :param int/str pId: the sequential assigned to a phase
1696    :returns:  (phase,ranId) where phase is the name of the phase (str)
1697      and ranId is the random # id for the phase (int)
1698    '''
1699    if not PhaseIdLookup:
1700        raise Exception('Error: LookupPhaseName called before IndexAllIds was run')
1701    if pId is None or pId == '':
1702        raise KeyError('Error: phase is invalid (None or blank)')
1703    pId = str(pId)
1704    if pId not in PhaseIdLookup:
1705        raise KeyError('Error: LookupPhaseName does not have index '+pId)
1706    return PhaseIdLookup[pId]
1707
1708def LookupHistId(ranId):
1709    '''Get the histogram number and name from a histogram random Id
1710
1711    :param int ranId: the random Id assigned to a histogram
1712    :returns: the sequential Id (hId) number for the histogram (str)
1713    '''
1714    if not HistRanIdLookup:
1715        raise Exception('Error: LookupHistId called before IndexAllIds was run')
1716    if ranId not in HistRanIdLookup:
1717        raise KeyError('Error: LookupHistId does not have ranId '+str(ranId))
1718    return HistRanIdLookup[ranId]
1719
1720def LookupHistName(hId):
1721    '''Get the histogram number and name from a histogram Id
1722
1723    :param int/str hId: the sequential assigned to a histogram
1724    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1725      and ranId is the random # id for the histogram (int)
1726    '''
1727    if not HistIdLookup:
1728        raise Exception('Error: LookupHistName called before IndexAllIds was run')
1729    if hId is None or hId == '':
1730        raise KeyError('Error: histogram is invalid (None or blank)')
1731    hId = str(hId)
1732    if hId not in HistIdLookup:
1733        raise KeyError('Error: LookupHistName does not have index '+hId)
1734    return HistIdLookup[hId]
1735
1736def fmtVarDescr(varname):
1737    '''Return a string with a more complete description for a GSAS-II variable
1738
1739    :param str varname: A full G2 variable name with 2 or 3 or 4
1740       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1741
1742    :returns: a string with the description
1743    '''
1744    s,l = VarDescr(varname)
1745    return s+": "+l
1746
1747def VarDescr(varname):
1748    '''Return two strings with a more complete description for a GSAS-II variable
1749
1750    :param str name: A full G2 variable name with 2 or 3 or 4
1751       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1752
1753    :returns: (loc,meaning) where loc describes what item the variable is mapped
1754      (phase, histogram, etc.) and meaning describes what the variable does.
1755    '''
1756
1757    # special handling for parameter names without a colon
1758    # for now, assume self-defining
1759    if varname.find(':') == -1:
1760        return "Global",varname
1761
1762    l = getVarDescr(varname)
1763    if not l:
1764        return ("invalid variable name ("+str(varname)+")!"),""
1765#        return "invalid variable name!",""
1766
1767    if not l[-1]:
1768        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1769
1770    if len(l) == 3:         #SASD variable name!
1771        s = 'component:'+l[1]
1772        return s,l[-1]
1773    s = ""
1774    if l[0] is not None and l[1] is not None: # HAP: keep short
1775        if l[2] == "Scale": # fix up ambigous name
1776            l[5] = "Phase fraction"
1777        if l[0] == '*':
1778            lbl = 'Seq. ref.'
1779        else:
1780            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1781        if l[1] == '*':
1782            hlbl = 'Seq. ref.'
1783        else:
1784            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1785        if hlbl[:4] == 'HKLF':
1786            hlbl = 'Xtl='+hlbl[5:]
1787        elif hlbl[:4] == 'PWDR':
1788            hlbl = 'Pwd='+hlbl[5:]
1789        else:
1790            hlbl = 'Hist='+hlbl
1791        s = "Ph="+str(lbl)+" * "+str(hlbl)
1792    else:
1793        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1794            l[5] = "Scale factor"
1795        if l[2] == 'Back': # background parameters are "special", alas
1796            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1797            l[-1] += ' #'+str(l[3])
1798        elif l[4] is not None: # rigid body parameter or modulation parm
1799            lbl = ShortPhaseNames.get(l[0],'phase?')
1800            if 'RB' in l[2]:    #rigid body parm
1801                s = "RB body #"+str(l[3])+" (type "+str(l[4])+") in "+str(lbl) + ','
1802            else: #modulation parm
1803                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1804        elif l[3] is not None: # atom parameter,
1805            lbl = ShortPhaseNames.get(l[0],'phase?')
1806            try:
1807                albl = LookupAtomLabel(l[0],l[3])[0]
1808            except KeyError:
1809                albl = 'Atom?'
1810            s = "Atom "+str(albl)+" in "+str(lbl)
1811        elif l[0] == '*':
1812            s = "All phases "
1813        elif l[0] is not None:
1814            lbl = ShortPhaseNames.get(l[0],'phase?')
1815            s = "Phase "+str(lbl)
1816        elif l[1] == '*':
1817            s = 'All hists'
1818        elif l[1] is not None:
1819            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1820            if hlbl[:4] == 'HKLF':
1821                hlbl = 'Xtl='+hlbl[5:]
1822            elif hlbl[:4] == 'PWDR':
1823                hlbl = 'Pwd='+hlbl[5:]
1824            else:
1825                hlbl = 'Hist='+hlbl
1826            s = str(hlbl)
1827    if not s:
1828        s = 'Global'
1829    return s,l[-1]
1830
1831def getVarDescr(varname):
1832    '''Return a short description for a GSAS-II variable
1833
1834    :param str name: A full G2 variable name with 2 or 3 or 4
1835       colons (<p>:<h>:name[:<a1>][:<a2>])
1836
1837    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1838      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1839      the histogram number and the atom number; `name` will always be
1840      a str; and `description` is str or `None`.
1841      If the variable name is incorrectly formed (for example, wrong
1842      number of colons), `None` is returned instead of a list.
1843    '''
1844    l = varname.split(':')
1845    if len(l) == 2:     #SASD parameter name
1846        return varname,l[0],getDescr(l[1])
1847    if len(l) == 3:
1848        l += [None,None]
1849    elif len(l) == 4:
1850        l += [None]
1851    elif len(l) != 5:
1852        return None
1853    for i in (0,1,3,4):
1854        if l[i] == "":
1855            l[i] = None
1856    l += [getDescr(l[2])]
1857    return l
1858
1859def CompileVarDesc():
1860    '''Set the values in the variable lookup tables
1861    (:attr:`reVarDesc` and :attr:`reVarStep`).
1862    This is called in :func:`getDescr` and :func:`getVarStep` so this
1863    initialization is always done before use.
1864
1865    Note that keys may contain regular expressions, where '[xyz]'
1866    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range
1867    of values). '.*' matches any string. For example::
1868
1869    'AUiso':'Atomic isotropic displacement parameter',
1870
1871    will match variable ``'p::AUiso:a'``.
1872    If parentheses are used in the key, the contents of those parentheses can be
1873    used in the value, such as::
1874
1875    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1876
1877    will match ``AU11``, ``AU23``,... and `U11`, `U23` etc will be displayed
1878    in the value when used.
1879
1880    '''
1881    if reVarDesc: return # already done
1882    for key,value in {
1883        # derived or other sequential vars
1884        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1885        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1886        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1887        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1888        # ambiguous, alas:
1889        'Scale' : 'Phase or Histogram scale factor',
1890        # Phase vars (p::<var>)
1891        'A([0-5])' : ('Reciprocal metric tensor component \\1',1e-5),
1892        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1893        # Atom vars (p::<var>:a)
1894        'dA([xyz])$' : ('change to atomic coordinate, \\1',1e-6),
1895        'A([xyz])$' : '\\1 fractional atomic coordinate',
1896        'AUiso':('Atomic isotropic displacement parameter',1e-4),
1897        'AU([123][123])':('Atomic anisotropic displacement parameter U\\1',1e-4),
1898        'Afrac': ('Atomic site fraction parameter',1e-5),
1899        'Amul': 'Atomic site multiplicity value',
1900        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1901        # Hist (:h:<var>) & Phase (HAP) vars (p:h:<var>)
1902        'Back': 'Background term',
1903        'BkPkint;(.*)':'Background peak #\\1 intensity',
1904        'BkPkpos;(.*)':'Background peak #\\1 position',
1905        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1906        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1907#        'Back File' : 'Background file name',
1908        'BF mult' : 'Background file multiplier',
1909        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1910        'D([123][123])' : 'Anisotropic strain coef. \\1',
1911        'Extinction' : 'Extinction coef.',
1912        'MD' : 'March-Dollase coef.',
1913        'Mustrain;.*' : 'Microstrain coef.',
1914        'Size;.*' : 'Crystallite size value',
1915        'eA$' : 'Cubic mustrain value',
1916        'Ep$' : 'Primary extinction',
1917        'Es$' : 'Secondary type II extinction',
1918        'Eg$' : 'Secondary type I extinction',
1919        'Flack' : 'Flack parameter',
1920        'TwinFr' : 'Twin fraction',
1921        'Layer Disp'  : 'Layer displacement along beam',
1922        #Histogram vars (:h:<var>)
1923        'Absorption' : 'Absorption coef.',
1924        'LayerDisp'  : 'Bragg-Brentano Layer displacement',
1925        'Displace([XY])' : ('Debye-Scherrer sample displacement \\1',0.1),
1926        'Lam' : ('Wavelength',1e-6),
1927        'I\\(L2\\)\\/I\\(L1\\)' : ('Ka2/Ka1 intensity ratio',0.001),
1928        'Polariz\\.' : ('Polarization correction',1e-3),
1929        'SH/L' : ('FCJ peak asymmetry correction',1e-4),
1930        '([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),
1931        '([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),
1932        'Zero' : 'Debye-Scherrer zero correction',
1933        'Shift' : 'Bragg-Brentano sample displ.',
1934        'SurfRoughA' : 'Bragg-Brenano surface roughness A',
1935        'SurfRoughB' : 'Bragg-Brenano surface roughness B',
1936        'Transparency' : 'Bragg-Brentano sample tranparency',
1937        'DebyeA' : 'Debye model amplitude',
1938        'DebyeR' : 'Debye model radius',
1939        'DebyeU' : 'Debye model Uiso',
1940        'RBV.*' : 'Vector rigid body parameter',
1941        'RBVO([aijk])' : 'Vector rigid body orientation parameter \\1',
1942        'RBVP([xyz])' : 'Vector rigid body \\1 position parameter',
1943        'RBVf' : 'Vector rigid body site fraction',
1944        'RBV([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1945        'RBVU' : 'Residue rigid body group Uiso param.',
1946        'RBRO([aijk])' : 'Residue rigid body orientation parameter \\1',
1947        'RBRP([xyz])' : 'Residue rigid body \\1 position parameter',
1948        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1949        'RBRf' : 'Residue rigid body site fraction',
1950        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1951        'RBRU' : 'Residue rigid body group Uiso param.',
1952        'constr([0-9]*)' : 'Parameter from constraint',
1953        'nv-([^_]+)_*' : 'New variable constraint parameter named \\1',
1954        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1955        'mV([0-2])$' : 'Modulation vector component \\1',
1956        'Fsin'  :   'Sin site fraction modulation',
1957        'Fcos'  :   'Cos site fraction modulation',
1958        'Fzero'  :   'Crenel function offset',      #may go away
1959        'Fwid'   :   'Crenel function width',
1960        'Tmin'   :   'ZigZag/Block min location',
1961        'Tmax'   :   'ZigZag/Block max location',
1962        '([XYZ])max': 'ZigZag/Block max value for \\1',
1963        '([XYZ])sin'  : 'Sin position wave for \\1',
1964        '([XYZ])cos'  : 'Cos position wave for \\1',
1965        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1966        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1967        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1968        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1969        # PDF peak parms (l:<var>;l = peak no.)
1970        'PDFpos'  : 'PDF peak position',
1971        'PDFmag'  : 'PDF peak magnitude',
1972        'PDFsig'  : 'PDF peak std. dev.',
1973        # SASD vars (l:<var>;l = component)
1974        'Aspect ratio' : 'Particle aspect ratio',
1975        'Length' : 'Cylinder length',
1976        'Diameter' : 'Cylinder/disk diameter',
1977        'Thickness' : 'Disk thickness',
1978        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1979        'Dist' : 'Interparticle distance',
1980        'VolFr' : 'Dense scatterer volume fraction',
1981        'epis' : 'Sticky sphere epsilon',
1982        'Sticky' : 'Stickyness',
1983        'Depth' : 'Well depth',
1984        'Width' : 'Well width',
1985        'Volume' : 'Particle volume',
1986        'Radius' : 'Sphere/cylinder/disk radius',
1987        'Mean' : 'Particle mean radius',
1988        'StdDev' : 'Standard deviation in Mean',
1989        'G$': 'Guinier prefactor',
1990        'Rg$': 'Guinier radius of gyration',
1991        'B$': 'Porod prefactor',
1992        'P$': 'Porod power',
1993        'Cutoff': 'Porod cutoff',
1994        'PkInt': 'Bragg peak intensity',
1995        'PkPos': 'Bragg peak position',
1996        'PkSig': 'Bragg peak sigma',
1997        'PkGam': 'Bragg peak gamma',
1998        'e([12][12])' : 'strain tensor e\\1',   # strain vars e11, e22, e12
1999        'Dcalc': 'Calc. d-spacing',
2000        'Back$': 'background parameter',
2001        'pos$': 'peak position',
2002        'int$': 'peak intensity',
2003        'WgtFrac':'phase weight fraction',
2004        'alpha':'TOF profile term',
2005        'alpha-[01]':'Pink profile term',
2006        'beta-[01q]':'TOF/Pink profile term',
2007        'sig-[012q]':'TOF profile term',
2008        'dif[ABC]':'TOF to d-space calibration',
2009        'C\\([0-9]*,[0-9]*\\)' : 'spherical harmonics preferred orientation coef.',
2010        'Pressure': 'Pressure level for measurement in MPa',
2011        'Temperature': 'T value for measurement, K',
2012        'FreePrm([123])': 'User defined measurement parameter \\1',
2013        'Gonio. radius': 'Distance from sample to detector, mm',
2014        }.items():
2015        # Needs documentation: HAP: LeBail, newLeBail
2016        # hist: Azimuth, Chi, Omega, Phi, Bank, nDebye, nPeaks
2017       
2018        if len(value) == 2:
2019            #VarDesc[key] = value[0]
2020            reVarDesc[re.compile(key)] = value[0]
2021            reVarStep[re.compile(key)] = value[1]
2022        else:
2023            #VarDesc[key] = value
2024            reVarDesc[re.compile(key)] = value
2025
2026def removeNonRefined(parmList):
2027    '''Remove items from variable list that are not refined and should not
2028    appear as options for constraints
2029
2030    :param list parmList: a list of strings of form "p:h:VAR:a" where
2031      VAR is the variable name
2032
2033    :returns: a list after removing variables where VAR matches a
2034      entry in local variable NonRefinedList
2035    '''
2036    NonRefinedList = ['Omega','Type','Chi','Phi', 'Azimuth','Gonio. radius',
2037                          'Lam1','Lam2','Back','Temperature','Pressure',
2038                          'FreePrm1','FreePrm2','FreePrm3',
2039                          'Source','nPeaks','LeBail','newLeBail','Bank',
2040                          'nDebye', #'',
2041                    ]
2042    return [prm for prm in parmList if prm.split(':')[2] not in NonRefinedList]
2043       
2044def getDescr(name):
2045    '''Return a short description for a GSAS-II variable
2046
2047    :param str name: The descriptive part of the variable name without colons (:)
2048
2049    :returns: a short description or None if not found
2050    '''
2051
2052    CompileVarDesc() # compile the regular expressions, if needed
2053    for key in reVarDesc:
2054        m = key.match(name)
2055        if m:
2056            reVarDesc[key]
2057            return m.expand(reVarDesc[key])
2058    return None
2059
2060def getVarStep(name,parmDict=None):
2061    '''Return a step size for computing the derivative of a GSAS-II variable
2062
2063    :param str name: A complete variable name (with colons, :)
2064    :param dict parmDict: A dict with parameter values or None (default)
2065
2066    :returns: a float that should be an appropriate step size, either from
2067      the value supplied in :func:`CompileVarDesc` or based on the value for
2068      name in parmDict, if supplied. If not found or the value is zero,
2069      a default value of 1e-5 is used. If parmDict is None (default) and
2070      no value is provided in :func:`CompileVarDesc`, then None is returned.
2071    '''
2072    CompileVarDesc() # compile the regular expressions, if needed
2073    for key in reVarStep:
2074        m = key.match(name)
2075        if m:
2076            return reVarStep[key]
2077    if parmDict is None: return None
2078    val = parmDict.get(key,0.0)
2079    if abs(val) > 0.05:
2080        return abs(val)/1000.
2081    else:
2082        return 1e-5
2083
2084def GenWildCard(varlist):
2085    '''Generate wildcard versions of G2 variables. These introduce '*'
2086    for a phase, histogram or atom number (but only for one of these
2087    fields) but only when there is more than one matching variable in the
2088    input variable list. So if the input is this::
2089
2090      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
2091
2092    then the output will be this::
2093
2094       wildList = ['*::AUiso:0', '0::AUiso:*']
2095
2096    :param list varlist: an input list of GSAS-II variable names
2097      (such as 0::AUiso:0)
2098
2099    :returns: wildList, the generated list of wild card variable names.
2100    '''
2101    wild = []
2102    for i in (0,1,3):
2103        currentL = varlist[:]
2104        while currentL:
2105            item1 = currentL.pop(0)
2106            i1splt = item1.split(':')
2107            if i >= len(i1splt): continue
2108            if i1splt[i]:
2109                nextL = []
2110                i1splt[i] = '[0-9]+'
2111                rexp = re.compile(':'.join(i1splt))
2112                matchlist = [item1]
2113                for nxtitem in currentL:
2114                    if rexp.match(nxtitem):
2115                        matchlist += [nxtitem]
2116                    else:
2117                        nextL.append(nxtitem)
2118                if len(matchlist) > 1:
2119                    i1splt[i] = '*'
2120                    wild.append(':'.join(i1splt))
2121                currentL = nextL
2122    return wild
2123
2124def LookupWildCard(varname,varlist):
2125    '''returns a list of variable names from list varname
2126    that match wildcard name in varname
2127
2128    :param str varname: a G2 variable name containing a wildcard
2129      (such as \\*::var)
2130    :param list varlist: the list of all variable names used in
2131      the current project
2132    :returns: a list of matching GSAS-II variables (may be empty)
2133    '''
2134    rexp = re.compile(varname.replace('*','[0-9]+'))
2135    return sorted([var for var in varlist if rexp.match(var)])
2136
2137def prmLookup(name,prmDict):
2138    '''Looks for a parameter in a min/max dictionary, optionally
2139    considering a wild card for histogram or atom number (use of
2140    both will never occur at the same time).
2141
2142    :param name: a GSAS-II parameter name (str, see :func:`getVarDescr`
2143      and :func:`CompileVarDesc`) or a :class:`G2VarObj` object.
2144    :param dict prmDict: a min/max dictionary, (parmMinDict
2145      or parmMaxDict in Controls) where keys are :class:`G2VarObj`
2146      objects.
2147    :returns: Two values, (**matchname**, **value**), are returned where:
2148
2149       * **matchname** *(str)* is the :class:`G2VarObj` object
2150         corresponding to the actual matched name,
2151         which could contain a wildcard even if **name** does not; and
2152       * **value** *(float)* which contains the parameter limit.
2153    '''
2154    for key,value in prmDict.items():
2155        if str(key) == str(name): return key,value
2156        if key == name: return key,value
2157    return None,None
2158       
2159
2160def _lookup(dic,key):
2161    '''Lookup a key in a dictionary, where None returns an empty string
2162    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
2163    '''
2164    if key is None:
2165        return ""
2166    elif key == "*":
2167        return "*"
2168    else:
2169        return dic.get(key,'?')
2170
2171def SortVariables(varlist):
2172    '''Sorts variable names in a sensible manner
2173    '''
2174    def cvnnums(var):
2175        v = []
2176        for i in var.split(':'):
2177#            if i == '' or i == '*':
2178#                v.append(-1)
2179#                continue
2180            try:
2181                v.append(int(i))
2182            except:
2183                v.append(-1)
2184        return v
2185    return sorted(varlist,key=cvnnums)
2186
2187class G2VarObj(object):
2188    '''Defines a GSAS-II variable either using the phase/atom/histogram
2189    unique Id numbers or using a character string that specifies
2190    variables by phase/atom/histogram number (which can change).
2191    Note that :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`,
2192    which calls :func:`IndexAllIds` (or
2193    :func:`GSASIIscriptable.G2Project.index_ids`) should be used to
2194    (re)load the current Ids
2195    before creating or later using the G2VarObj object.
2196
2197    This can store rigid body variables, but does not translate the residue # and
2198    body # to/from random Ids
2199
2200    A :class:`G2VarObj` object can be created with a single parameter:
2201
2202    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
2203      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
2204
2205     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
2206     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
2207     * a is the atom number (which may be left blank in which case the third colon is omitted).
2208       The atom number can be specified as '*' if a phase number is specified (not as '*').
2209       For rigid body variables, specify a will be a string of form "residue:body#"
2210
2211      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
2212      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
2213      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
2214      For a rigid body variables, AtomID is a string of form "residue:body#".
2215
2216    If four positional arguments are supplied, they are:
2217
2218    :param str/int phasenum: The number for the phase (or None or '*')
2219    :param str/int histnum: The number for the histogram (or None or '*')
2220    :param str varname: a single value can be used to create a :class:`G2VarObj`
2221    :param str/int atomnum: The number for the atom (or None or '*')
2222
2223    '''
2224    IDdict = {}
2225    IDdict['phases'] = {}
2226    IDdict['hists'] = {}
2227    IDdict['atoms'] = {}
2228    def __init__(self,*args):
2229        self.phase = None
2230        self.histogram = None
2231        self.name = ''
2232        self.atom = None
2233        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
2234            # single arg with 4 values
2235            self.phase,self.histogram,self.name,self.atom = args[0]
2236        elif len(args) == 1 and ':' in args[0]:
2237            #parse a string
2238            lst = args[0].split(':')
2239            if lst[0] == '*':
2240                self.phase = '*'
2241                if len(lst) > 3:
2242                    self.atom = lst[3]
2243                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2244            elif lst[1] == '*':
2245                self.histogram = '*'
2246                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2247            else:
2248                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2249                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2250                if len(lst) == 4:
2251                    if lst[3] == '*':
2252                        self.atom = '*'
2253                    else:
2254                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
2255                elif len(lst) == 5:
2256                    self.atom = lst[3]+":"+lst[4]
2257                elif len(lst) == 3:
2258                    pass
2259                else:
2260                    raise Exception("Incorrect number of colons in var name "+str(args[0]))
2261            self.name = lst[2]
2262        elif len(args) == 4:
2263            if args[0] == '*':
2264                self.phase = '*'
2265                self.atom = args[3]
2266            else:
2267                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
2268                if args[3] == '*':
2269                    self.atom = '*'
2270                elif args[0] is not None:
2271                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
2272            if args[1] == '*':
2273                self.histogram = '*'
2274            else:
2275                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
2276            self.name = args[2]
2277        else:
2278            raise Exception("Incorrectly called GSAS-II parameter name")
2279
2280        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
2281
2282    def __str__(self):
2283        return self.varname()
2284
2285    def __hash__(self):
2286        'Allow G2VarObj to be a dict key by implementing hashing'
2287        return hash(self.varname())
2288
2289    def varname(self,hist=None):
2290        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
2291        string (p:h:<var>:a) or (p:h:<var>)
2292
2293        :param str/int hist: if specified, overrides the histogram number
2294          with the specified value
2295        :returns: the variable name as a str
2296        '''
2297        a = ""
2298        if self.phase == "*":
2299            ph = "*"
2300            if self.atom:
2301                a = ":" + str(self.atom)
2302        else:
2303            ph = _lookup(PhaseRanIdLookup,self.phase)
2304            if self.atom == '*':
2305                a = ':*'
2306            elif self.atom:
2307                if ":" in str(self.atom):
2308                    a = ":" + str(self.atom)
2309                elif ph in AtomRanIdLookup:
2310                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
2311                else:
2312                    a = ":?"
2313        if hist is not None and self.histogram:
2314            hist = str(hist)
2315        elif self.histogram == "*":
2316            hist = "*"
2317        else:
2318            hist = _lookup(HistRanIdLookup,self.histogram)
2319        s = (ph + ":" + hist + ":" + str(self.name)) + a
2320        return s
2321
2322    def __repr__(self):
2323        '''Return the detailed contents of the object
2324        '''
2325        s = "<"
2326        if self.phase == '*':
2327            s += "Phases: all; "
2328            if self.atom is not None:
2329                if ":" in str(self.atom):
2330                    s += "Rigid body" + str(self.atom) + "; "
2331                else:
2332                    s += "Atom #" + str(self.atom) + "; "
2333        elif self.phase is not None:
2334            ph =  _lookup(PhaseRanIdLookup,self.phase)
2335            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
2336            if self.atom == '*':
2337                s += "Atoms: all; "
2338            elif ":" in str(self.atom):
2339                s += "Rigid body" + str(self.atom) + "; "
2340            elif self.atom is not None:
2341                s += "Atom rId=" + str(self.atom)
2342                if ph in AtomRanIdLookup:
2343                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
2344                else:
2345                    s += " (#? -- not found!); "
2346        if self.histogram == '*':
2347            s += "Histograms: all; "
2348        elif self.histogram is not None:
2349            hist = _lookup(HistRanIdLookup,self.histogram)
2350            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
2351        s += 'Variable name="' + str(self.name) + '">'
2352        return s+" ("+self.varname()+")"
2353
2354    def __eq__(self, other):
2355        '''Allow comparison of G2VarObj to other G2VarObj objects or strings.
2356        If any field is a wildcard ('*') that field matches.
2357        '''
2358        if type(other) is str:
2359            other = G2VarObj(other)
2360        elif type(other) is not G2VarObj:
2361            raise Exception("Invalid type ({}) for G2VarObj comparison with {}"
2362                            .format(type(other),other))
2363        if self.phase != other.phase and self.phase != '*' and other.phase != '*':
2364            return False
2365        if self.histogram != other.histogram and self.histogram != '*' and other.histogram != '*':
2366            return False
2367        if self.atom != other.atom and self.atom != '*' and other.atom != '*':
2368            return False
2369        if self.name != other.name:
2370            return False
2371        return True
2372   
2373    def fmtVarByMode(self, seqmode, note, warnmsg):
2374        '''Format a parameter object for display. Note that these changes
2375        are only temporary and are only shown only when the Constraints
2376        data tree is selected.
2377
2378        * In a non-sequential refinement or where the mode is 'use-all', the
2379          name is converted unchanged to a str
2380        * In a sequential refinement when the mode is 'wildcards-only' the
2381          name is converted unchanged to a str but a warning is added
2382          for non-wildcarded HAP or Histogram parameters
2383        * In a sequential refinement or where the mode is 'auto-wildcard',
2384          a histogram number is converted to a wildcard (*) and then
2385          converted to str
2386
2387        :param str mode: the sequential mode (see above)
2388        :param str note: value displayed on the line of the constraint/equiv.
2389        :param str warnmsg: a message saying the constraint is not used
2390
2391        :returns: varname, explain, note, warnmsg (all str values) where:
2392          * varname is the parameter expressed as a string,
2393          * explain is blank unless there is a warning explanation about
2394            the parameter or blank
2395          * note is the previous value unless overridden
2396          * warnmsg is the previous value unless overridden
2397        '''
2398        explain = ''
2399        s = self.varname()
2400        if seqmode == 'auto-wildcard':
2401            if self.histogram: s = self.varname('*')
2402        elif seqmode == 'wildcards-only' and self.histogram:
2403            if self.histogram != '*':
2404                warnmsg = 'Ignored due to use of a non-wildcarded histogram number'
2405                note = 'Ignored'
2406                explain = '\nIgnoring: '+self.varname()+' does not contain a wildcard.\n'
2407        elif seqmode != 'use-all' and seqmode != 'wildcards-only':
2408            print('Unexpected mode',seqmode,' in fmtVarByMode')
2409        return s,explain,note,warnmsg
2410
2411    def _show(self):
2412        'For testing, shows the current lookup table'
2413        print ('phases'+ self.IDdict['phases'])
2414        print ('hists'+ self.IDdict['hists'])
2415        print ('atomDict'+ self.IDdict['atoms'])
2416
2417#==========================================================================
2418def SetDefaultSample():
2419    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
2420    return {
2421        'InstrName':'',
2422        'ranId':ran.randint(0,sys.maxsize),
2423        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
2424        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],
2425        'Temperature':300.,'Pressure':0.1,'Time':0.0,
2426        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
2427        'Gonio. radius':200.0,
2428        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
2429#SASD items
2430        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
2431        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
2432        'Trans':1.0,                            #measured transmission
2433        'SlitLen':0.0,                          #Slit length - in Q(A-1)
2434        }
2435######################################################################
2436class ImportBaseclass(object):
2437    '''Defines a base class for the reading of input files (diffraction
2438    data, coordinates,...). See :ref:`Writing a Import Routine<import_routines>`
2439    for an explanation on how to use a subclass of this class.
2440    '''
2441    class ImportException(Exception):
2442        '''Defines an Exception that is used when an import routine hits an expected error,
2443        usually in .Reader.
2444
2445        Good practice is that the Reader should define a value in self.errors that
2446        tells the user some information about what is wrong with their file.
2447        '''
2448        pass
2449
2450    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
2451    def __init__(self,formatName,longFormatName=None,
2452                 extensionlist=[],strictExtension=False,):
2453        self.formatName = formatName # short string naming file type
2454        if longFormatName: # longer string naming file type
2455            self.longFormatName = longFormatName
2456        else:
2457            self.longFormatName = formatName
2458        # define extensions that are allowed for the file type
2459        # for windows, remove any extensions that are duplicate, as case is ignored
2460        if sys.platform == 'windows' and extensionlist:
2461            extensionlist = list(set([s.lower() for s in extensionlist]))
2462        self.extensionlist = extensionlist
2463        # If strictExtension is True, the file will not be read, unless
2464        # the extension matches one in the extensionlist
2465        self.strictExtension = strictExtension
2466        self.errors = ''
2467        self.warnings = ''
2468        self.SciPy = False          #image reader needed scipy
2469        # used for readers that will use multiple passes to read
2470        # more than one data block
2471        self.repeat = False
2472        self.selections = []
2473        self.repeatcount = 0
2474        self.readfilename = '?'
2475        self.scriptable = False
2476        #print 'created',self.__class__
2477
2478    def ReInitialize(self):
2479        'Reinitialize the Reader to initial settings'
2480        self.errors = ''
2481        self.warnings = ''
2482        self.SciPy = False          #image reader needed scipy
2483        self.repeat = False
2484        self.repeatcount = 0
2485        self.readfilename = '?'
2486
2487
2488#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
2489#        '''This method must be supplied in the child class to read the file.
2490#        if the read fails either return False or raise an Exception
2491#        preferably of type ImportException.
2492#        '''
2493#        #start reading
2494#        raise ImportException("Error occurred while...")
2495#        self.errors += "Hint for user on why the error occur
2496#        return False # if an error occurs
2497#        return True # if read OK
2498
2499    def ExtensionValidator(self, filename):
2500        '''This methods checks if the file has the correct extension
2501       
2502        :returns:
2503       
2504          * False if this filename will not be supported by this reader (only
2505            when strictExtension is True)
2506          * True if the extension matches the list supplied by the reader
2507          * None if the reader allows un-registered extensions
2508         
2509        '''
2510        if filename:
2511            ext = ospath.splitext(filename)[1]
2512            if not ext and self.strictExtension: return False
2513            for ext in self.extensionlist:               
2514                if sys.platform == 'windows':
2515                    if filename.lower().endswith(ext): return True
2516                else:
2517                    if filename.endswith(ext): return True
2518        if self.strictExtension:
2519            return False
2520        else:
2521            return None
2522
2523    def ContentsValidator(self, filename):
2524        '''This routine will attempt to determine if the file can be read
2525        with the current format.
2526        This will typically be overridden with a method that
2527        takes a quick scan of [some of]
2528        the file contents to do a "sanity" check if the file
2529        appears to match the selected format.
2530        the file must be opened here with the correct format (binary/text)
2531        '''
2532        #filepointer.seek(0) # rewind the file pointer
2533        return True
2534
2535    def CIFValidator(self, filepointer):
2536        '''A :meth:`ContentsValidator` for use to validate CIF files.
2537        '''
2538        filepointer.seek(0)
2539        for i,l in enumerate(filepointer):
2540            if i >= 1000: return True
2541            '''Encountered only blank lines or comments in first 1000
2542            lines. This is unlikely, but assume it is CIF anyway, since we are
2543            even less likely to find a file with nothing but hashes and
2544            blank lines'''
2545            line = l.strip()
2546            if len(line) == 0: # ignore blank lines
2547                continue
2548            elif line.startswith('#'): # ignore comments
2549                continue
2550            elif line.startswith('data_'): # on the right track, accept this file
2551                return True
2552            else: # found something invalid
2553                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
2554                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
2555                    self.errors += '  '+str(l)
2556                else:
2557                    self.errors += '  (binary)'
2558                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
2559                self.errors += '\n        a data_ statement begins a block.'
2560                return False
2561
2562######################################################################
2563class ImportPhase(ImportBaseclass):
2564    '''Defines a base class for the reading of files with coordinates
2565
2566    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
2567    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` and in
2568    :func:`GSASIIscriptable.import_generic`.
2569    See :ref:`Writing a Import Routine<import_routines>`
2570    for an explanation on how to use this class.
2571
2572    '''
2573    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2574        strictExtension=False,):
2575        # call parent __init__
2576        ImportBaseclass.__init__(self,formatName,longFormatName,
2577            extensionlist,strictExtension)
2578        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
2579        self.SymOps = {} # specified when symmetry ops are in file (e.g. CIF)
2580        self.Constraints = None
2581
2582######################################################################
2583class ImportStructFactor(ImportBaseclass):
2584    '''Defines a base class for the reading of files with tables
2585    of structure factors.
2586
2587    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
2588    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
2589    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2590    :meth:`Reader`.
2591
2592    See :ref:`Writing a Import Routine<import_routines>`
2593    for an explanation on how to use import classes in general. The specifics
2594    for reading a structure factor histogram require that
2595    the ``Reader()`` routine in the import
2596    class need to do only a few things: It
2597    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2598    and set :attr:`Parameters` with the instrument parameters
2599    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2600    '''
2601    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2602        strictExtension=False,):
2603        ImportBaseclass.__init__(self,formatName,longFormatName,
2604            extensionlist,strictExtension)
2605
2606        # define contents of Structure Factor entry
2607        self.Parameters = []
2608        'self.Parameters is a list with two dicts for data parameter settings'
2609        self.InitParameters()
2610        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2611        self.Banks = []             #for multi bank data (usually TOF)
2612        '''self.RefDict is a dict containing the reflection information, as read from the file.
2613        Item 'RefList' contains the reflection information. See the
2614        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
2615        for the contents of each row. Dict element 'FF'
2616        contains the form factor values for each element type; if this entry
2617        is left as initialized (an empty list) it will be initialized as needed later.
2618        '''
2619    def ReInitialize(self):
2620        'Reinitialize the Reader to initial settings'
2621        ImportBaseclass.ReInitialize(self)
2622        self.InitParameters()
2623        self.Banks = []             #for multi bank data (usually TOF)
2624        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2625
2626    def InitParameters(self):
2627        'initialize the instrument parameters structure'
2628        Lambda = 0.70926
2629        HistType = 'SXC'
2630        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2631                            'Lam':[Lambda,Lambda]
2632                            }, {}]
2633        'Parameters is a list with two dicts for data parameter settings'
2634
2635    def UpdateParameters(self,Type=None,Wave=None):
2636        'Revise the instrument parameters'
2637        if Type is not None:
2638            self.Parameters[0]['Type'] = [Type,Type]
2639        if Wave is not None:
2640            self.Parameters[0]['Lam'] = [Wave,Wave]
2641
2642######################################################################
2643class ImportPowderData(ImportBaseclass):
2644    '''Defines a base class for the reading of files with powder data.
2645
2646    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2647    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder` and in
2648    :func:`GSASIIscriptable.import_generic`.
2649    See :ref:`Writing a Import Routine<import_routines>`
2650    for an explanation on how to use this class.
2651    '''
2652    def __init__(self,formatName,longFormatName=None,
2653        extensionlist=[],strictExtension=False,):
2654        ImportBaseclass.__init__(self,formatName,longFormatName,
2655            extensionlist,strictExtension)
2656        self.clockWd = None  # used in TOF
2657        self.ReInitialize()
2658
2659    def ReInitialize(self):
2660        'Reinitialize the Reader to initial settings'
2661        ImportBaseclass.ReInitialize(self)
2662        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2663        self.powderdata = [] # Powder dataset
2664        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2665                np.array(x), # x-axis values
2666                np.array(y), # powder pattern intensities
2667                np.array(w), # 1/sig(intensity)^2 values (weights)
2668                np.array(yc), # calc. intensities (zero)
2669                np.array(yb), # calc. background (zero)
2670                np.array(yd), # obs-calc profiles
2671        '''
2672        self.comments = []
2673        self.idstring = ''
2674        self.Sample = SetDefaultSample() # default sample parameters
2675        self.Controls = {}  # items to be placed in top-level Controls
2676        self.GSAS = None     # used in TOF
2677        self.repeat_instparm = True # Should a parm file be
2678        #                             used for multiple histograms?
2679        self.instparm = None # name hint from file of instparm to use
2680        self.instfile = '' # full path name to instrument parameter file
2681        self.instbank = '' # inst parm bank number
2682        self.instmsg = ''  # a label that gets printed to show
2683                           # where instrument parameters are from
2684        self.numbanks = 1
2685        self.instdict = {} # place items here that will be transferred to the instrument parameters
2686        self.pwdparms = {} # place parameters that are transferred directly to the tree
2687                           # here (typically from an existing GPX file)
2688######################################################################
2689class ImportSmallAngleData(ImportBaseclass):
2690    '''Defines a base class for the reading of files with small angle data.
2691    See :ref:`Writing a Import Routine<import_routines>`
2692    for an explanation on how to use this class.
2693    '''
2694    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2695        strictExtension=False,):
2696
2697        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2698            strictExtension)
2699        self.ReInitialize()
2700
2701    def ReInitialize(self):
2702        'Reinitialize the Reader to initial settings'
2703        ImportBaseclass.ReInitialize(self)
2704        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2705        self.smallangledata = [] # SASD dataset
2706        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2707                np.array(x), # x-axis values
2708                np.array(y), # powder pattern intensities
2709                np.array(w), # 1/sig(intensity)^2 values (weights)
2710                np.array(yc), # calc. intensities (zero)
2711                np.array(yd), # obs-calc profiles
2712                np.array(yb), # preset bkg
2713        '''
2714        self.comments = []
2715        self.idstring = ''
2716        self.Sample = SetDefaultSample()
2717        self.GSAS = None     # used in TOF
2718        self.clockWd = None  # used in TOF
2719        self.numbanks = 1
2720        self.instdict = {} # place items here that will be transferred to the instrument parameters
2721
2722######################################################################
2723class ImportReflectometryData(ImportBaseclass):
2724    '''Defines a base class for the reading of files with reflectometry data.
2725    See :ref:`Writing a Import Routine<import_routines>`
2726    for an explanation on how to use this class.
2727    '''
2728    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2729        strictExtension=False,):
2730
2731        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2732            strictExtension)
2733        self.ReInitialize()
2734
2735    def ReInitialize(self):
2736        'Reinitialize the Reader to initial settings'
2737        ImportBaseclass.ReInitialize(self)
2738        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2739        self.reflectometrydata = [] # SASD dataset
2740        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2741                np.array(x), # x-axis values
2742                np.array(y), # powder pattern intensities
2743                np.array(w), # 1/sig(intensity)^2 values (weights)
2744                np.array(yc), # calc. intensities (zero)
2745                np.array(yd), # obs-calc profiles
2746                np.array(yb), # preset bkg
2747        '''
2748        self.comments = []
2749        self.idstring = ''
2750        self.Sample = SetDefaultSample()
2751        self.GSAS = None     # used in TOF
2752        self.clockWd = None  # used in TOF
2753        self.numbanks = 1
2754        self.instdict = {} # place items here that will be transferred to the instrument parameters
2755
2756######################################################################
2757class ImportPDFData(ImportBaseclass):
2758    '''Defines a base class for the reading of files with PDF G(R) data.
2759    See :ref:`Writing a Import Routine<import_routines>`
2760    for an explanation on how to use this class.
2761    '''
2762    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2763        strictExtension=False,):
2764
2765        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2766            strictExtension)
2767        self.ReInitialize()
2768
2769    def ReInitialize(self):
2770        'Reinitialize the Reader to initial settings'
2771        ImportBaseclass.ReInitialize(self)
2772        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2773        self.pdfdata = [] # PDF G(R) dataset
2774        '''A pdf g(r) data set is a list with items [x,y]:
2775                np.array(x), # r-axis values
2776                np.array(y), # pdf g(r)
2777        '''
2778        self.comments = []
2779        self.idstring = ''
2780        self.numbanks = 1
2781
2782######################################################################
2783class ImportImage(ImportBaseclass):
2784    '''Defines a base class for the reading of images
2785
2786    Images are read in only these places:
2787
2788      * Initial reading is typically done from a menu item
2789        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2790        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2791        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2792        :meth:`Reader`. This returns a list of reader objects for each read image.
2793        Also used in :func:`GSASIIscriptable.import_generic`.
2794
2795      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2796        directly into the data tree.
2797
2798      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2799
2800    When reading an image, the ``Reader()`` routine in the ImportImage class
2801    should set:
2802
2803      * :attr:`Comments`: a list of strings (str),
2804      * :attr:`Npix`: the number of pixels in the image (int),
2805      * :attr:`Image`: the actual image as a numpy array (np.array)
2806      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2807        data items are needed:
2808
2809         * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2810         * 'wavelength': wavelength in :math:`\\AA`.
2811         * 'distance': distance of detector from sample in cm.
2812         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2813         * 'size': size of image (such as ``[2048,2048]``).
2814         * 'ImageTag': image number or other keyword used to retrieve image from
2815           a multi-image data file (defaults to ``1`` if not specified).
2816         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2817
2818    optional data items:
2819
2820      * :attr:`repeat`: set to True if there are additional images to
2821        read in the file, False otherwise
2822      * :attr:`repeatcount`: set to the number of the image.
2823
2824    Note that the above is initialized with :meth:`InitParameters`.
2825    (Also see :ref:`Writing a Import Routine<import_routines>`
2826    for an explanation on how to use import classes in general.)
2827    '''
2828    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2829        strictExtension=False,):
2830        ImportBaseclass.__init__(self,formatName,longFormatName,
2831            extensionlist,strictExtension)
2832        self.InitParameters()
2833
2834    def ReInitialize(self):
2835        'Reinitialize the Reader to initial settings -- not used at present'
2836        ImportBaseclass.ReInitialize(self)
2837        self.InitParameters()
2838
2839    def InitParameters(self):
2840        'initialize the instrument parameters structure'
2841        self.Comments = ['No comments']
2842        self.Data = {'samplechangerpos':0.0,'det2theta':0.0,'Gain map':''}
2843        self.Npix = 0
2844        self.Image = None
2845        self.repeat = False
2846        self.repeatcount = 1
2847        self.sumfile = ''
2848
2849    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2850        '''Optionally, call this after reading in an image to load it into the tree.
2851        This saves time by preventing a reread of the same information.
2852        '''
2853        if ParentFrame:
2854            ParentFrame.ImageZ = self.Image   # store the image for plotting
2855            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2856            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2857
2858#################################################################################################
2859# shortcut routines
2860exp = np.exp
2861sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2862cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2863tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2864sqrt = sq = lambda x: np.sqrt(x)
2865pi = lambda: np.pi
2866
2867def FindFunction(f):
2868    '''Find the object corresponding to function f
2869
2870    :param str f: a function name such as 'numpy.exp'
2871    :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2872      that defines the package location(s) and where pkgobj
2873      defines the object associated with the function.
2874      If the function is not found, pkgobj is None.
2875    '''
2876    df = f.split('.')
2877    pkgdict = {}
2878    # no listed module name, try in current namespace
2879    if len(df) == 1:
2880        try:
2881            fxnobj = eval(f)
2882            return pkgdict,fxnobj
2883        except (AttributeError, NameError):
2884            return None,None
2885
2886    # includes a package, see if package is already imported
2887    pkgnam = '.'.join(df[:-1])
2888    try:
2889        fxnobj = eval(f)
2890        pkgdict[pkgnam] = eval(pkgnam)
2891        return pkgdict,fxnobj
2892    except (AttributeError, NameError):
2893        pass
2894    # package not yet imported, so let's try
2895    if '.' not in sys.path: sys.path.append('.')
2896    pkgnam = '.'.join(df[:-1])
2897    #for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2898    #    if pkgname:
2899    #        pkgname += '.' + pkg
2900    #    else:
2901    #        pkgname = pkg
2902    try:
2903        exec('import '+pkgnam)
2904        pkgdict[pkgnam] = eval(pkgnam)
2905        fxnobj = eval(f)
2906    except Exception as msg:
2907        print('load of '+pkgnam+' failed with error='+str(msg))
2908        return {},None
2909    # can we access the function? I am not exactly sure what
2910    #    I intended this to test originally (BHT)
2911    try:
2912        fxnobj = eval(f,globals(),pkgdict)
2913        return pkgdict,fxnobj
2914    except Exception as msg:
2915        print('call to',f,' failed with error=',str(msg))
2916        return None,None # not found
2917               
2918class ExpressionObj(object):
2919    '''Defines an object with a user-defined expression, to be used for
2920    secondary fits or restraints. Object is created null, but is changed
2921    using :meth:`LoadExpression`. This contains only the minimum
2922    information that needs to be stored to save and load the expression
2923    and how it is mapped to GSAS-II variables.
2924    '''
2925    def __init__(self):
2926        self.expression = ''
2927        'The expression as a text string'
2928        self.assgnVars = {}
2929        '''A dict where keys are label names in the expression mapping to a GSAS-II
2930        variable. The value a G2 variable name.
2931        Note that the G2 variable name may contain a wild-card and correspond to
2932        multiple values.
2933        '''
2934        self.freeVars = {}
2935        '''A dict where keys are label names in the expression mapping to a free
2936        parameter. The value is a list with:
2937
2938         * a name assigned to the parameter
2939         * a value for to the parameter and
2940         * a flag to determine if the variable is refined.
2941        '''
2942        self.depVar = None
2943
2944        self.lastError = ('','')
2945        '''Shows last encountered error in processing expression
2946        (list of 1-3 str values)'''
2947
2948        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2949        self.distance_atoms = None  # to be used for defining atom distances
2950
2951    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2952        '''Load the expression and associated settings into the object. Raises
2953        an exception if the expression is not parsed, if not all functions
2954        are defined or if not all needed parameter labels in the expression
2955        are defined.
2956
2957        This will not test if the variable referenced in these definitions
2958        are actually in the parameter dictionary. This is checked when the
2959        computation for the expression is done in :meth:`SetupCalc`.
2960
2961        :param str expr: the expression
2962        :param list exprVarLst: parameter labels found in the expression
2963        :param dict varSelect: this will be 0 for Free parameters
2964          and non-zero for expression labels linked to G2 variables.
2965        :param dict varName: Defines a name (str) associated with each free parameter
2966        :param dict varValue: Defines a value (float) associated with each free parameter
2967        :param dict varRefflag: Defines a refinement flag (bool)
2968          associated with each free parameter
2969        '''
2970        self.expression = expr
2971        self.compiledExpr = None
2972        self.freeVars = {}
2973        self.assgnVars = {}
2974        for v in exprVarLst:
2975            if varSelect[v] == 0:
2976                self.freeVars[v] = [
2977                    varName.get(v),
2978                    varValue.get(v),
2979                    varRefflag.get(v),
2980                    ]
2981            else:
2982                self.assgnVars[v] = varName[v]
2983        self.CheckVars()
2984
2985    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2986        '''Load the expression and associated settings from the object into
2987        arrays used for editing.
2988
2989        :param list exprVarLst: parameter labels found in the expression
2990        :param dict varSelect: this will be 0 for Free parameters
2991          and non-zero for expression labels linked to G2 variables.
2992        :param dict varName: Defines a name (str) associated with each free parameter
2993        :param dict varValue: Defines a value (float) associated with each free parameter
2994        :param dict varRefflag: Defines a refinement flag (bool)
2995          associated with each free parameter
2996
2997        :returns: the expression as a str
2998        '''
2999        for v in self.freeVars:
3000            varSelect[v] = 0
3001            varName[v] = self.freeVars[v][0]
3002            varValue[v] = self.freeVars[v][1]
3003            varRefflag[v] = self.freeVars[v][2]
3004        for v in self.assgnVars:
3005            varSelect[v] = 1
3006            varName[v] = self.assgnVars[v]
3007        return self.expression
3008
3009    def GetVaried(self):
3010        'Returns the names of the free parameters that will be refined'
3011        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
3012
3013    def GetVariedVarVal(self):
3014        'Returns the names and values of the free parameters that will be refined'
3015        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
3016
3017    def UpdateVariedVars(self,varyList,values):
3018        'Updates values for the free parameters (after a refinement); only updates refined vars'
3019        for v in self.freeVars:
3020            if not self.freeVars[v][2]: continue
3021            if "::"+self.freeVars[v][0] not in varyList: continue
3022            indx = list(varyList).index("::"+self.freeVars[v][0])
3023            self.freeVars[v][1] = values[indx]
3024
3025    def GetIndependentVars(self):
3026        'Returns the names of the required independent parameters used in expression'
3027        return [self.assgnVars[v] for v in self.assgnVars]
3028
3029    def CheckVars(self):
3030        '''Check that the expression can be parsed, all functions are
3031        defined and that input loaded into the object is internally
3032        consistent. If not an Exception is raised.
3033
3034        :returns: a dict with references to packages needed to
3035          find functions referenced in the expression.
3036        '''
3037        ret = self.ParseExpression(self.expression)
3038        if not ret:
3039            raise Exception("Expression parse error")
3040        exprLblList,fxnpkgdict = ret
3041        # check each var used in expression is defined
3042        defined = list(self.assgnVars.keys()) + list(self.freeVars.keys())
3043        notfound = []
3044        for var in exprLblList:
3045            if var not in defined:
3046                notfound.append(var)
3047        if notfound:
3048            msg = 'Not all variables defined'
3049            msg1 = 'The following variables were not defined: '
3050            msg2 = ''
3051            for var in notfound:
3052                if msg: msg += ', '
3053                msg += var
3054            self.lastError = (msg1,'  '+msg2)
3055            raise Exception(msg)
3056        return fxnpkgdict
3057
3058    def ParseExpression(self,expr):
3059        '''Parse an expression and return a dict of called functions and
3060        the variables used in the expression. Returns None in case an error
3061        is encountered. If packages are referenced in functions, they are loaded
3062        and the functions are looked up into the modules global
3063        workspace.
3064
3065        Note that no changes are made to the object other than
3066        saving an error message, so that this can be used for testing prior
3067        to the save.
3068
3069        :returns: a list of used variables
3070        '''
3071        self.lastError = ('','')
3072        import ast
3073        def ASTtransverse(node,fxn=False):
3074            '''Transverse a AST-parsed expresson, compiling a list of variables
3075            referenced in the expression. This routine is used recursively.
3076
3077            :returns: varlist,fxnlist where
3078              varlist is a list of referenced variable names and
3079              fxnlist is a list of used functions
3080            '''
3081            varlist = []
3082            fxnlist = []
3083            if isinstance(node, list):
3084                for b in node:
3085                    v,f = ASTtransverse(b,fxn)
3086                    varlist += v
3087                    fxnlist += f
3088            elif isinstance(node, ast.AST):
3089                for a, b in ast.iter_fields(node):
3090                    if isinstance(b, ast.AST):
3091                        if a == 'func':
3092                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
3093                            continue
3094                        v,f = ASTtransverse(b,fxn)
3095                        varlist += v
3096                        fxnlist += f
3097                    elif isinstance(b, list):
3098                        v,f = ASTtransverse(b,fxn)
3099                        varlist += v
3100                        fxnlist += f
3101                    elif node.__class__.__name__ == "Name":
3102                        varlist += [b]
3103                    elif fxn and node.__class__.__name__ == "Attribute":
3104                        varlist += [b]
3105            return varlist,fxnlist
3106        try:
3107            exprast = ast.parse(expr)
3108        except SyntaxError:
3109            s = ''
3110            import traceback
3111            for i in traceback.format_exc().splitlines()[-3:-1]:
3112                if s: s += "\n"
3113                s += str(i)
3114            self.lastError = ("Error parsing expression:",s)
3115            return
3116        # find the variables & functions
3117        v,f = ASTtransverse(exprast)
3118        varlist = sorted(list(set(v)))
3119        fxnlist = list(set(f))
3120        pkgdict = {}
3121        # check the functions are defined
3122        for fxn in fxnlist:
3123            fxndict,fxnobj = FindFunction(fxn)
3124            if not fxnobj:
3125                self.lastError = ("Error: Invalid function",fxn,
3126                                  "is not defined")
3127                return
3128            if not hasattr(fxnobj,'__call__'):
3129                self.lastError = ("Error: Not a function.",fxn,
3130                                  "cannot be called as a function")
3131                return
3132            pkgdict.update(fxndict)
3133        return varlist,pkgdict
3134
3135    def GetDepVar(self):
3136        'return the dependent variable, or None'
3137        return self.depVar
3138
3139    def SetDepVar(self,var):
3140        'Set the dependent variable, if used'
3141        self.depVar = var
3142#==========================================================================
3143class ExpressionCalcObj(object):
3144    '''An object used to evaluate an expression from a :class:`ExpressionObj`
3145    object.
3146
3147    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
3148      an expression string and mappings for the parameter labels in that object.
3149    '''
3150    def __init__(self,exprObj):
3151        self.eObj = exprObj
3152        'The expression and mappings; a :class:`ExpressionObj` object'
3153        self.compiledExpr = None
3154        'The expression as compiled byte-code'
3155        self.exprDict = {}
3156        '''dict that defines values for labels used in expression and packages
3157        referenced by functions
3158        '''
3159        self.lblLookup = {}
3160        '''Lookup table that specifies the expression label name that is
3161        tied to a particular GSAS-II parameters in the parmDict.
3162        '''
3163        self.fxnpkgdict = {}
3164        '''a dict with references to packages needed to
3165        find functions referenced in the expression.
3166        '''
3167        self.varLookup = {}
3168        '''Lookup table that specifies the GSAS-II variable(s)
3169        indexed by the expression label name. (Used for only for diagnostics
3170        not evaluation of expression.)
3171        '''
3172        self.su = None
3173        '''Standard error evaluation where supplied by the evaluator
3174        '''
3175        # Patch: for old-style expressions with a (now removed step size)
3176        if '2' in platform.python_version_tuple()[0]: 
3177            basestr = basestring
3178        else:
3179            basestr = str
3180        for v in self.eObj.assgnVars:
3181            if not isinstance(self.eObj.assgnVars[v], basestr):
3182                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
3183        self.parmDict = {}
3184        '''A copy of the parameter dictionary, for distance and angle computation
3185        '''
3186
3187    def SetupCalc(self,parmDict):
3188        '''Do all preparations to use the expression for computation.
3189        Adds the free parameter values to the parameter dict (parmDict).
3190        '''
3191        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3192            return
3193        self.fxnpkgdict = self.eObj.CheckVars()
3194        # all is OK, compile the expression
3195        self.compiledExpr = compile(self.eObj.expression,'','eval')
3196
3197        # look at first value in parmDict to determine its type
3198        parmsInList = True
3199        if '2' in platform.python_version_tuple()[0]: 
3200            basestr = basestring
3201        else:
3202            basestr = str
3203        for key in parmDict:
3204            val = parmDict[key]
3205            if isinstance(val, basestr):
3206                parmsInList = False
3207                break
3208            try: # check if values are in lists
3209                val = parmDict[key][0]
3210            except (TypeError,IndexError):
3211                parmsInList = False
3212            break
3213
3214        # set up the dicts needed to speed computations
3215        self.exprDict = {}
3216        self.lblLookup = {}
3217        self.varLookup = {}
3218        for v in self.eObj.freeVars:
3219            varname = self.eObj.freeVars[v][0]
3220            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
3221            self.lblLookup[varname] = v
3222            self.varLookup[v] = varname
3223            if parmsInList:
3224                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
3225            else:
3226                parmDict[varname] = self.eObj.freeVars[v][1]
3227            self.exprDict[v] = self.eObj.freeVars[v][1]
3228        for v in self.eObj.assgnVars:
3229            varname = self.eObj.assgnVars[v]
3230            if varname in parmDict:
3231                self.lblLookup[varname] = v
3232                self.varLookup[v] = varname
3233                if parmsInList:
3234                    self.exprDict[v] = parmDict[varname][0]
3235                else:
3236                    self.exprDict[v] = parmDict[varname]
3237            elif '*' in varname:
3238                varlist = LookupWildCard(varname,list(parmDict.keys()))
3239                if len(varlist) == 0:
3240                    raise Exception("No variables match "+str(v))
3241                for var in varlist:
3242                    self.lblLookup[var] = v
3243                if parmsInList:
3244                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
3245                else:
3246                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
3247                self.varLookup[v] = [var for var in varlist]
3248            else:
3249                self.exprDict[v] = None
3250#                raise Exception,"No value for variable "+str(v)
3251        self.exprDict.update(self.fxnpkgdict)
3252
3253    def UpdateVars(self,varList,valList):
3254        '''Update the dict for the expression with a set of values
3255        :param list varList: a list of variable names
3256        :param list valList: a list of corresponding values
3257        '''
3258        for var,val in zip(varList,valList):
3259            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
3260
3261    def UpdateDict(self,parmDict):
3262        '''Update the dict for the expression with values in a dict
3263        :param dict parmDict: a dict of values, items not in use are ignored
3264        '''
3265        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3266            self.parmDict = parmDict
3267            return
3268        for var in parmDict:
3269            if var in self.lblLookup:
3270                self.exprDict[self.lblLookup[var]] = parmDict[var]
3271
3272    def EvalExpression(self):
3273        '''Evaluate an expression. Note that the expression
3274        and mapping are taken from the :class:`ExpressionObj` expression object
3275        and the parameter values were specified in :meth:`SetupCalc`.
3276        :returns: a single value for the expression. If parameter
3277        values are arrays (for example, from wild-carded variable names),
3278        the sum of the resulting expression is returned.
3279
3280        For example, if the expression is ``'A*B'``,
3281        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
3282
3283        [0.5, 1, 0.5]
3284
3285        then the result will be ``4.0``.
3286        '''
3287        self.su = None
3288        if self.eObj.expression.startswith('Dist'):
3289#            GSASIIpath.IPyBreak()
3290            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
3291            return dist
3292        elif self.eObj.expression.startswith('Angle'):
3293            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
3294            return angle
3295        if self.compiledExpr is None:
3296            raise Exception("EvalExpression called before SetupCalc")
3297        try:
3298            val = eval(self.compiledExpr,globals(),self.exprDict)
3299        except TypeError:
3300            val = None
3301        if not np.isscalar(val):
3302            val = np.sum(val)
3303        return val
3304
3305class G2Exception(Exception):
3306    'A generic GSAS-II exception class'
3307    def __init__(self,msg):
3308        self.msg = msg
3309    def __str__(self):
3310        return repr(self.msg)
3311
3312class G2RefineCancel(Exception):
3313    'Raised when Cancel is pressed in a refinement dialog'
3314    def __init__(self,msg):
3315        self.msg = msg
3316    def __str__(self):
3317        return repr(self.msg)
3318   
3319def HowDidIgetHere(wherecalledonly=False):
3320    '''Show a traceback with calls that brought us to the current location.
3321    Used for debugging.
3322    '''
3323    import traceback
3324    if wherecalledonly:
3325        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
3326        print(i.strip().rstrip())
3327    else:
3328        print (70*'*')
3329        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
3330        print (70*'*')
3331
3332# Note that this is GUI code and should be moved at somepoint
3333def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
3334    '''Create and initialize a new set of PDF tree entries
3335
3336    :param Frame G2frame: main GSAS-II tree frame object
3337    :param str PWDRtree: name of PWDR to be used to create PDF item
3338    :param dict ElList: data structure with composition
3339    :param list Qlimits: Q limits to be used for computing the PDF
3340    :param float numAtm: no. atom in chemical formula
3341    :param float FltBkg: flat background value
3342    :param list PDFnames: previously used PDF names
3343
3344    :returns: the Id of the newly created PDF entry
3345    '''
3346    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
3347    if PDFname in PDFnames:
3348        print('Skipping, entry already exists: '+PDFname)
3349        return None
3350    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
3351    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
3352    Data = {
3353        'Sample':{'Name':PWDRtree,'Mult':1.0},
3354        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
3355        'Container':{'Name':'','Mult':-1.0,'Refine':False},
3356        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
3357        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
3358        'DetType':'Area detector','ObliqCoeff':0.3,'Ruland':0.025,'QScaleLim':Qlimits,
3359        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,'Rmin':1.0,
3360        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
3361    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
3362    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
3363        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
3364    return Id
3365
3366class ShowTiming(object):
3367    '''An object to use for timing repeated sections of code.
3368
3369    Create the object with::
3370       tim0 = ShowTiming()
3371
3372    Tag sections of code to be timed with::
3373       tim0.start('start')
3374       tim0.start('in section 1')
3375       tim0.start('in section 2')
3376       
3377    etc. (Note that each section should have a unique label.)
3378
3379    After the last section, end timing with::
3380       tim0.end()
3381
3382    Show timing results with::
3383       tim0.show()
3384       
3385    '''
3386    def __init__(self):
3387        self.timeSum =  []
3388        self.timeStart = []
3389        self.label = []
3390        self.prev = None
3391    def start(self,label):
3392        import time
3393        if label in self.label:
3394            i = self.label.index(label)
3395            self.timeStart[i] = time.time()
3396        else:
3397            i = len(self.label)
3398            self.timeSum.append(0.0)
3399            self.timeStart.append(time.time())
3400            self.label.append(label)
3401        if self.prev is not None:
3402            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
3403        self.prev = i
3404    def end(self):
3405        import time
3406        if self.prev is not None:
3407            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
3408        self.prev = None
3409    def show(self):
3410        sumT = sum(self.timeSum)
3411        print('Timing results (total={:.2f} sec)'.format(sumT))
3412        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
3413            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
3414
3415def validateAtomDrawType(typ,generalData={}):
3416    '''Confirm that the selected Atom drawing type is valid for the current
3417    phase. If not, use 'vdW balls'. This is currently used only for setting a
3418    default when atoms are added to the atoms draw list.
3419    '''
3420    if typ in ('lines','vdW balls','sticks','balls & sticks','ellipsoids'):
3421        return typ
3422    # elif generalData.get('Type','') == 'macromolecular':
3423    #     if typ in ('backbone',):
3424    #         return typ
3425    return 'vdW balls'
3426
3427if __name__ == "__main__":
3428    # test variable descriptions
3429    for var in '0::Afrac:*',':1:Scale','1::dAx:0','::undefined':
3430        v = var.split(':')[2]
3431        print(var+':\t', getDescr(v),getVarStep(v))
3432    import sys; sys.exit()
3433    # test equation evaluation
3434    def showEQ(calcobj):
3435        print (50*'=')
3436        print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
3437        for v in sorted(calcobj.varLookup):
3438            print ("  "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
3439        # print '  Derivatives'
3440        # for v in calcobj.derivStep.keys():
3441        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
3442
3443    obj = ExpressionObj()
3444
3445    obj.expression = "A*np.exp(B)"
3446    obj.assgnVars =  {'B': '0::Afrac:1'}
3447    obj.freeVars =  {'A': [u'A', 0.5, True]}
3448    #obj.CheckVars()
3449    calcobj = ExpressionCalcObj(obj)
3450
3451    obj1 = ExpressionObj()
3452    obj1.expression = "A*np.exp(B)"
3453    obj1.assgnVars =  {'B': '0::Afrac:*'}
3454    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
3455    #obj.CheckVars()
3456    calcobj1 = ExpressionCalcObj(obj1)
3457
3458    obj2 = ExpressionObj()
3459    obj2.distance_stuff = np.array([[0,1],[1,-1]])
3460    obj2.expression = "Dist(1,2)"
3461    GSASIIpath.InvokeDebugOpts()
3462    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3463    calcobj2 = ExpressionCalcObj(obj2)
3464    calcobj2.SetupCalc(parmDict2)
3465    showEQ(calcobj2)
3466
3467    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
3468    print ('\nDict = '+parmDict1)
3469    calcobj.SetupCalc(parmDict1)
3470    showEQ(calcobj)
3471    calcobj1.SetupCalc(parmDict1)
3472    showEQ(calcobj1)
3473
3474    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3475    print ('Dict = '+parmDict2)
3476    calcobj.SetupCalc(parmDict2)
3477    showEQ(calcobj)
3478    calcobj1.SetupCalc(parmDict2)
3479    showEQ(calcobj1)
3480    calcobj2.SetupCalc(parmDict2)
3481    showEQ(calcobj2)
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