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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2021-06-15 18:36:25 +0000 (Tue, 15 Jun 2021) $
5# $Author: vondreele $
6# $Revision: 4960 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 4960 2021-06-15 18:36:25Z vondreele $
9########### SVN repository information ###################
10
11'''
12*GSASIIobj: Data objects*
13=========================
14
15This module defines and/or documents the data structures used in GSAS-II, as well
16as provides misc. support routines.
17
18.. Next command allows \\AA to be used in HTML
19
20.. only:: html
21
22   :math:`\\require{mediawiki-texvc}`
23
24.. _Constraints_table:
25
26.. index::
27   single: Constraints object description
28   single: Data object descriptions; Constraints
29
30Constraints Tree Item
31----------------------
32
33Constraints are stored in a dict, separated into groups.
34Note that parameter are named in the following pattern,
35p:h:<var>:n, where p is the phase number, h is the histogram number
36<var> is a variable name and n is the parameter number.
37If a parameter does not depend on a histogram or phase or is unnumbered, that
38number is omitted.
39Note that the contents of each dict item is a List where each element in the
40list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
41The constraints in this form are converted in
42:func:`GSASIIstrIO.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
43
44The keys in the Constraints dict are:
45
46.. tabularcolumns:: |l|p{4.5in}|
47
48==========  ====================================================
49  key         explanation
50==========  ====================================================
51Hist        This specifies a list of constraints on
52            histogram-related parameters,
53            which will be of form :h:<var>:n.
54HAP         This specifies a list of constraints on parameters
55            that are defined for every histogram in each phase
56            and are of form p:h:<var>:n.
57Phase       This specifies a list of constraints on phase
58            parameters,
59            which will be of form p::<var>:n.
60Global      This specifies a list of constraints on parameters
61            that are not tied to a histogram or phase and
62            are of form ::<var>:n
63==========  ====================================================
64
65.. _Constraint_definitions_table:
66
67.. index::
68   single: Constraint definition object description
69   single: Data object descriptions; Constraint Definition
70
71Each constraint is defined as an item in a list. Each constraint is of form::
72
73[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
74
75Where the variable pair list item containing two values [<mult>, <var>], where:
76
77  * <mult> is a multiplier for the constraint (float)
78  * <var> a :class:`G2VarObj` object (previously a str variable name of form
79      'p:h:name[:at]')
80
81Note that the last three items in the list play a special role:
82
83 * <fixedval> is the fixed value for a `constant equation` (``constype=c``)
84   constraint or is None. For a `New variable` (``constype=f``) constraint,
85   a variable name can be specified as a str (used for externally
86   generated constraints)
87 * <varyflag> is True or False for `New variable` (``constype=f``) constraints
88   or is None. This indicates if this variable should be refined.
89 * <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
90
91    * 'e' defines a set of equivalent variables. Only the first variable is refined (if the
92      appropriate refine flag is set) and and all other equivalent variables in the list
93      are generated from that variable, using the appropriate multipliers.
94    * 'c' defines a constraint equation of form,
95      :math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
96    * 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
97      even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
98      constraint and the mult value is ignored.
99      This is of particular value when needing to hold one or more variables where a
100      single flag controls a set of variables such as, coordinates,
101      the reciprocal metric tensor or anisotropic displacement parameter.
102    * 'f' defines a new variable (function) according to relationship
103      :math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
104
105.. _Covariance_table:
106
107.. index::
108   single: Covariance description
109   single: Data object descriptions; Covariance
110
111Covariance Tree Item
112--------------------
113
114The Covariance tree item has results from the last least-squares run. They
115are stored in a dict with these keys:
116
117.. tabularcolumns:: |l|l|p{4in}|
118
119=============  ===============  ====================================================
120  key            sub-key        explanation
121=============  ===============  ====================================================
122newCellDict    \\                (dict) ith lattice parameters computed by
123                                :func:`GSASIIstrMath.GetNewCellParms`
124title          \\                (str) Name of gpx file(?)
125variables      \\                (list) Values for all N refined variables
126                                (list of float values, length N,
127                                ordered to match varyList)
128sig            \\                (list) Uncertainty values for all N refined variables
129                                (list of float values, length N,
130                                ordered to match varyList)
131varyList       \\                (list of str values, length N) List of directly refined variables
132                               
133newAtomDict    \\                (dict) atom position values computed in
134                                :func:`GSASIIstrMath.ApplyXYZshifts`
135Rvals          \\                (dict) R-factors, GOF, Marquardt value for last
136                                refinement cycle
137\\              Nobs             (int) Number of observed data points
138\\              Rwp              (float) overall weighted profile R-factor (%)
139\\              chisq            (float) :math:`\\sum w*(I_{obs}-I_{calc})^2`                               
140                                for all data.
141                                Note: this is not the reduced :math:`\\chi^2`.
142\\              lamMax           (float) Marquardt value applied to Hessian diagonal
143\\              GOF              (float) The goodness-of-fit, aka square root of
144                                the reduced chi squared.
145covMatrix      \\                (np.array) The (NxN) covVariance matrix
146=============  ===============  ====================================================
147
148.. _Phase_table:
149
150.. index::
151   single: Phase object description
152   single: Data object descriptions; Phase
153
154Phase Tree Items
155----------------
156
157Phase information is stored in the GSAS-II data tree as children of the
158Phases item in a dict with keys:
159
160.. tabularcolumns:: |l|l|p{4in}|
161
162==========  ===============     =====================================================================================================
163  key         sub-key           explanation
164==========  ===============     =====================================================================================================
165General         \\               (dict) Overall information for the phase
166  \\         3Dproj              (list of str) projections for 3D pole distribution plots
167  \\         AngleRadii          (list of floats) Default radius for each atom used to compute
168                                interatomic angles
169  \\         AtomMass            (list of floats) Masses for atoms
170  \\         AtomPtrs            (list of int) four locations (cx,ct,cs & cu) to use to pull info
171                                from the atom records
172  \\         AtomTypes           (llist of str) Atom types
173  \\         BondRadii           (list of floats) Default radius for each atom used to compute
174                                interatomic distances
175  \\         Cell                Unit cell parameters & ref. flag
176                                (list with 8 items. All but first item are float.)
177
178                                 0: cell refinement flag (True/False),
179                                 1-3: a, b, c, (:math:`\\AA`)
180                                 4-6: alpha, beta & gamma, (degrees)
181                                 7: volume (:math:`\\AA^3`)
182  \\         Color               (list of (r,b,g) triplets) Colors for atoms
183  \\         Compare             (dict) Polygon comparison parameters
184  \\         Data plot type      (str) data plot type ('Mustrain', 'Size' or
185                                'Preferred orientation') for powder data
186  \\         DisAglCtls          (dDict) with distance/angle search controls,
187                                which has keys 'Name', 'AtomTypes',
188                                'BondRadii', 'AngleRadii' which are as above
189                                except are possibly edited. Also contains
190                                'Factors', which is a 2 element list with
191                                a multiplier for bond and angle search range
192                                [typically (0.85,0.85)].
193  \\         F000X               (float) x-ray F(000) intensity
194  \\         F000N               (float) neutron F(000) intensity
195  \\         Flip                (dict) Charge flip controls
196  \\         HydIds              (dict) geometrically generated hydrogen atoms
197  \\         Isotope             (dict) Isotopes for each atom type
198  \\         Isotopes            (dict) Scattering lengths for each isotope
199                                combination for each element in phase
200  \\         MCSA controls       (dict) Monte Carlo-Simulated Annealing controls
201  \\         Map                 (dict) Map parameters
202  \\         Mass                (float) Mass of unit cell contents in g/mol
203  \\         Modulated           (bool) True if phase modulated
204  \\         Mydir               (str) Directory of current .gpx file
205  \\         Name                (str) Phase name
206  \\         NoAtoms             (dict) Number of atoms per unit cell of each type
207  \\         POhkl               (list) March-Dollase preferred orientation direction
208  \\         Pawley dmin         (float) maximum Q (as d-space) to use for Pawley extraction
209  \\         Pawley dmax         (float) minimum Q (as d-space) to use for Pawley extraction
210  \\         Pawley neg wt       (float) Restraint value for negative Pawley intensities
211  \\         SGData              (object) Space group details as a
212                                :ref:`space group (SGData) <SGData_table>`
213                                object, as defined in :func:`GSASIIspc.SpcGroup`.
214  \\         SH Texture          (dict) Spherical harmonic preferred orientation parameters
215  \\         Super               (int) dimension of super group (0,1 only)
216  \\         Type                (str) phase type (e.g. 'nuclear')
217  \\         Z                   (dict) Atomic numbers for each atom type
218  \\         doDysnomia          (bool) flag for max ent map modification via Dysnomia
219  \\         doPawley            (bool) Flag for Pawley intensity extraction
220  \\         vdWRadii            (dict) Van der Waals radii for each atom type
221ranId           \\               (int) unique random number Id for phase
222pId             \\               (int) Phase Id number for current project.
223Atoms           \\               (list of lists) Atoms in phase as a list of lists. The outer list
224                                is for each atom, the inner list contains varying
225                                items depending on the type of phase, see
226                                the :ref:`Atom Records <Atoms_table>` description.
227Drawing         \\               (dict) Display parameters
228\\           Atoms               (list of lists) with an entry for each atom that is drawn
229\\           Plane               (list) Controls for contour density plane display
230\\           Quaternion          (4 element np.array) Viewing quaternion
231\\           Zclip               (float) clipping distance in :math:`\\AA`
232\\           Zstep               (float) Step to de/increase Z-clip
233\\           atomPtrs            (list) positions of x, type, site sym, ADP flag in Draw Atoms
234\\           backColor           (list) background for plot as and R,G,B triplet
235                                (default = [0, 0, 0], black).
236\\           ballScale           (float) Radius of spheres in ball-and-stick display
237\\           bondList            (dict) Bonds
238\\           bondRadius          (float) Radius of binds in :math:`\\AA`
239\\           cameraPos           (float) Viewing position in :math:`\\AA` for plot
240\\           contourLevel        (float) map contour level in :math:`e/\\AA^3`
241\\           contourMax          (float) map contour maximum
242\\           depthFog            (bool) True if use depthFog on plot - set currently as False
243\\           ellipseProb         (float) Probability limit for display of thermal
244                                ellipsoids in % .
245\\           magMult             (float) multiplier for magnetic moment arrows
246\\           mapSize             (float) x & y dimensions of contourmap (fixed internally)
247\\           modelView           (4,4 array) from openGL drawing transofmation matrix
248\\           oldxy               (list with two floats) previous view point
249\\           radiusFactor        (float) Distance ratio for searching for bonds. Bonds
250                                are located that are within r(Ra+Rb) and (Ra+Rb)/r
251                                where Ra and Rb are the atomic radii.
252\\           selectedAtoms       (list of int values) List of selected atoms
253\\           showABC             (bool) Flag to show view point triplet. True=show.
254\\           showHydrogen        (bool) Flag to control plotting of H atoms.
255\\           showRigidBodies     (bool) Flag to highlight rigid body placement
256\\           showSlice           (bool) flag to show contour map
257\\           sizeH               (float) Size ratio for H atoms
258\\           unitCellBox         (bool) Flag to control display of the unit cell.
259\\           vdwScale            (float) Multiplier of van der Waals radius for display of vdW spheres.
260\\           viewDir             (np.array with three floats) cartesian viewing direction
261\\           viewPoint           (list of lists) First item in list is [x,y,z]
262                                in fractional coordinates for the center of
263                                the plot. Second item list of previous & current
264                                atom number viewed (may be [0,0])
265RBModels        \\               Rigid body assignments (note Rigid body definitions
266                                are stored in their own main top-level tree entry.)
267RMC             \\               (dict) RMCProfile & rmcfull controls
268Pawley ref      \\               (list) Pawley reflections
269Histograms      \\               (dict of dicts) The key for the outer dict is
270                                the histograms tied to this phase. The inner
271                                dict contains the combined phase/histogram
272                                parameters for items such as scale factors,
273                                size and strain parameters. The following are the
274                                keys to the inner dict. (dict)
275\\           Babinet             (dict) For protein crystallography. Dictionary with two
276                                entries, 'BabA', 'BabU'
277\\           Extinction          (list of float, bool) Extinction parameter
278\\           Flack               (list of [float, bool]) Flack parameter & refine flag
279\\           HStrain             (list of two lists) Hydrostatic strain. The first is
280                                a list of the HStrain parameters (1, 2, 3, 4, or 6
281                                depending on unit cell), the second is a list of boolean
282                                refinement parameters (same length)
283\\           Histogram           (str) The name of the associated histogram
284\\           Layer Disp          (list of [float, bool]) Layer displacement in beam direction & refine flag
285\\           LeBail              (bool) Flag for LeBail extraction
286\\           Mustrain            (list) Microstrain parameters, in order:
287   
288                                0. Type, one of  u'isotropic', u'uniaxial', u'generalized'
289                                1. Isotropic/uniaxial parameters - list of 3 floats
290                                2. Refinement flags - list of 3 bools
291                                3. Microstrain axis - list of 3 ints, [h, k, l]
292                                4. Generalized mustrain parameters - list of 2-6 floats, depending on space group
293                                5. Generalized refinement flags - list of bools, corresponding to the parameters of (4)
294\\           Pref.Ori.           (list) Preferred Orientation. List of eight parameters.
295                                Items marked SH are only used for Spherical Harmonics.
296                               
297                                0. (str) Type, 'MD' for March-Dollase or 'SH' for Spherical Harmonics
298                                1. (float) Value
299                                2. (bool) Refinement flag
300                                3. (list) Preferred direction, list of ints, [h, k, l]
301                                4. (int) SH - number of terms
302                                5. (dict) SH - 
303                                6. (list) SH
304                                7. (float) SH
305\\           Scale               (list of [float, bool]) Phase fraction & refine flag
306\\           Size                List of crystallite size parameters, in order:
307
308                                0. (str) Type, one of  u'isotropic', u'uniaxial', u'ellipsoidal'
309                                1. (list) Isotropic/uniaxial parameters - list of 3 floats
310                                2. (list) Refinement flags - list of 3 bools
311                                3. (list) Size axis - list of 3 ints, [h, k, l]
312                                4. (list) Ellipsoidal size parameters - list of 6 floats
313                                5. (list) Ellipsoidal refinement flags - list of bools, corresponding to the parameters of (4)
314\\           Use                 (bool) True if this histogram is to be used in refinement
315\\           newLeBail           (bool) Whether to perform a new LeBail extraction
316MCSA            \\               (dict) Monte-Carlo simulated annealing parameters
317==========  ===============     =====================================================================================================
318
319.. _RBData_table:
320
321.. index::
322   single: Rigid Body Data description
323   single: Data object descriptions; Rigid Body Data
324
325Rigid Body Objects
326------------------
327
328Rigid body descriptions are available for two types of rigid bodies: 'Vector'
329and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
330with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
331with defined refinable torsion angles.
332
333.. tabularcolumns:: |l|l|p{4in}|
334
335==========  ===============     ====================================================
336  key         sub-key           explanation
337==========  ===============     ====================================================
338Vector      RBId                (dict of dict) vector rigid bodies
339\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
340\\           RBname              (str) Name assigned by user to rigid body
341\\           VectMag             (list) vector magnitudes in :math:`\\AA`
342\\           rbXYZ               (list of 3 float Cartesian coordinates for Vector rigid body )
343\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
344                                definition, use center of atoms flag
345\\           VectRef             (list of bool refinement flags for VectMag values )
346\\           rbTypes             (list of str) Atom types for each atom in rigid body
347\\           rbVect              (list of lists) Cartesian vectors for each translation used to build rigid body
348\\           useCount            (int) Number of times rigid body is used in any structure
349Residue     RBId                (dict of dict) residue rigid bodies
350\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
351\\           RBname              (str) Name assigned by user to rigid body
352\\           rbXYZ               (list of 3 float) Cartesian coordinates for Residue rigid body
353\\           rbTypes             (list of str) Atom types for each atom in rigid body
354\\           atNames             (list of str) Names of each atom in rigid body (e.g. C1,N2...)
355\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
356                                definition, use center of atoms flag
357\\           rbSeq               (list) Orig,Piv,angle,Riding : definition of internal rigid body
358                                torsion; origin atom (int), pivot atom (int), torsion angle (float),
359                                riding atoms (list of int)
360\\           SelSeq              (int,int) used by SeqSizer to identify objects
361\\           useCount            (int)Number of times rigid body is used in any structure
362RBIds           \\               (dict) unique Ids generated upon creation of each rigid body
363\\           Vector              (list) Ids for each Vector rigid body
364\\           Residue             (list) Ids for each Residue rigid body
365==========  ===============     ====================================================
366
367.. _SGData_table:
368
369.. index::
370   single: Space Group Data description
371   single: Data object descriptions; Space Group Data
372
373Space Group Objects
374-------------------
375
376Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
377and the information is placed in a SGdata object
378which is a dict with these keys. Magnetic ones are marked "mag"
379
380.. tabularcolumns:: |l|p{4.5in}|
381
382==========  ========================================================================================
383  key         explanation
384==========  ========================================================================================
385BNSlattsym  mag - (str) BNS magnetic space group symbol and centering vector
386GenFlg      mag - (list) symmetry generators indices
387GenSym      mag - (list) names for each generator
388MagMom      mag - (list) "time reversals" for each magnetic operator
389MagPtGp     mag - (str) Magnetic point group symbol
390MagSpGrp    mag - (str) Magnetic space group symbol
391OprNames    mag - (list) names for each space group operation
392SGCen       (np.array) Symmetry cell centering vectors. A (n,3) np.array
393            of centers. Will always have at least one row: ``np.array([[0, 0, 0]])``
394SGFixed     (bool) Only True if phase mported from a magnetic cif file
395            then the space group can not be changed by the user because
396            operator set from cif may be nonstandard
397SGGen       (list) generators
398SGGray      (bool) True if space group is a gray group (incommensurate magnetic structures)
399SGInv       (bool) True if centrosymmetric, False if not
400SGLatt      (str)Lattice centering type. Will be one of
401            P, A, B, C, I, F, R
402SGLaue      (str) one of the following 14 Laue classes:
403            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
404            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m
405SGOps       (list) symmetry operations as a list of form
406            ``[[M1,T1], [M2,T2],...]``
407            where :math:`M_n` is a 3x3 np.array
408            and :math:`T_n` is a length 3 np.array.
409            Atom coordinates are transformed where the
410            Asymmetric unit coordinates [X is (x,y,z)]
411            are transformed using
412            :math:`X^\\prime = M_n*X+T_n`
413SGPolax     (str) Axes for space group polarity. Will be one of
414            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
415            'xyz'. In the case where axes are arbitrary
416            '111' is used (P 1, and ?).
417SGPtGrp     (str) Point group of the space group
418SGUniq      unique axis if monoclinic. Will be
419            a, b, or c for monoclinic space groups.
420            Will be blank for non-monoclinic.
421SGSpin      mag - (list) of spin flip operatiors (+1 or -1) for the space group operations
422SGSys       (str) symmetry unit cell: type one of
423            'triclinic', 'monoclinic', 'orthorhombic',
424            'tetragonal', 'rhombohedral', 'trigonal',
425            'hexagonal', 'cubic'
426SSGK1       (list) Superspace multipliers
427SpGrp       (str) space group symbol
428SpnFlp      mag - (list) Magnetic spin flips for every magnetic space group operator
429==========  ========================================================================================
430
431.. _SSGData_table:
432
433.. index::
434   single: Superspace Group Data description
435   single: Data object descriptions; Superspace Group Data
436
437Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
438and the information is placed in a SSGdata object
439which is a dict with these keys:
440
441.. tabularcolumns:: |l|p{4.5in}|
442
443==========  ====================================================
444  key         explanation
445==========  ====================================================
446SSGCen      (list) 4D cell centering vectors [0,0,0,0] at least
447SSGK1       (list) Superspace multipliers
448SSGOps      (list) 4D symmetry operations as [M,T] so that M*x+T = x'
449SSpGrp      (str) superspace group symbol extension to space group
450            symbol, accidental spaces removed
451modQ        (list) modulation/propagation vector
452modSymb     (list of str) Modulation symbols
453==========  ====================================================
454
455
456Phase Information
457--------------------
458
459.. index::
460   single: Phase information record description
461
462Phase information is placed in one of the following keys:
463
464.. tabularcolumns:: |l|p{4.5in}|
465
466==========  ==============================================================
467  key         explanation
468==========  ==============================================================
469General       Overall information about a phase
470Histograms    Information about each histogram linked to the
471              current phase as well as parameters that
472              are defined for each histogram and phase
473              (such as sample peak widths and preferred
474              orientation parameters.
475Atoms         Contains a list of atoms, as described in the
476              :ref:`Atom Records <Atoms_table>` description.
477Drawing       Parameters that determine how the phase is
478              displayed, including a list of atoms to be
479              included, as described in the
480              :ref:`Drawing Atom Records <Drawing_atoms_table>`
481              description
482MCSA          Monte-Carlo simulated annealing parameters
483pId           The index of each phase in the project, numbered
484              starting at 0
485ranId         An int value with a unique value for each phase
486RBModels      A list of dicts with parameters for each
487              rigid body inserted into the current phase,
488              as defined in the
489              :ref:`Rigid Body Insertions <Rigid_Body_Insertions>`.
490              Note that the rigid bodies are defined as
491              :ref:`Rigid Body Objects <RBData_table>`
492RMC           PDF modeling parameters
493Pawley ref    Pawley refinement parameters
494
495==========  ==============================================================
496
497.. _Atoms_table:
498
499.. index::
500   single: Atoms record description
501   single: Data object descriptions; Atoms record
502
503--------------------
504Atom Records
505--------------------
506
507If ``phasedict`` points to the phase information in the data tree, then
508atoms are contained in a list of atom records (list) in
509``phasedict['Atoms']``. Also needed to read atom information
510are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
511which define locations in the atom record, as shown below. Items shown are
512always present; additional ones for macromolecular phases are marked 'mm',
513and those for magnetic structures are marked 'mg'
514
515.. tabularcolumns:: |l|p{4.5in}|
516
517==============      ====================================================
518location            explanation
519==============      ====================================================
520ct-4                mm - (str) residue number
521ct-3                mm - (str) residue name (e.g. ALA)
522ct-2                mm - (str) chain label
523ct-1                (str) atom label
524ct                  (str) atom type
525ct+1                (str) refinement flags; combination of 'F', 'X', 'U', 'M'
526cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
527cx+3                (float) site occupancy
528cx+4,cx+5,cx+6      mg - (list) atom magnetic moment along a,b,c in Bohr magnetons
529cs                  (str) site symmetry
530cs+1                (int) site multiplicity
531cia                 (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
532cia+1               (float) Uiso
533cia+2...cia+7       (6 floats) U11, U22, U33, U12, U13, U23
534atom[cia+8]         (int) unique atom identifier
535
536==============      ====================================================
537
538.. _Drawing_atoms_table:
539
540.. index::
541   single: Drawing atoms record description
542   single: Data object descriptions; Drawing atoms record
543
544----------------------------
545Drawing Atom Records
546----------------------------
547
548If ``phasedict`` points to the phase information in the data tree, then
549drawing atoms are contained in a list of drawing atom records (list) in
550``phasedict['Drawing']['Atoms']``. Also needed to read atom information
551are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
552which define locations in the atom record, as shown below. Items shown are
553always present; additional ones for macromolecular phases are marked 'mm',
554and those for magnetic structures are marked 'mg'
555
556.. tabularcolumns:: |l|p{4.5in}|
557
558==============   ===================================================================================
559location            explanation
560==============   ===================================================================================
561ct-4                mm - (str) residue number
562ct-3                mm - (str) residue name (e.g. ALA)
563ct-2                mm - (str) chain label
564ct-1                (str) atom label
565ct                  (str) atom type
566cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
567cx+3,cx+4,cx+5      mg - (3 floats) atom magnetic moment along a,b,c in Bohr magnetons
568cs-1                (str) Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1')
569cs                  (str) atom drawing style; e.g. 'balls & sticks'
570cs+1                (str) atom label style (e.g. 'name')
571cs+2                (int) atom color (RBG triplet)
572cs+3                (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
573cs+4                (float) Uiso
574cs+5...cs+11        (6 floats) U11, U22, U33, U12, U13, U23
575ci                  (int) unique atom identifier; matches source atom Id in Atom Records
576==============   ===================================================================================
577
578.. _Rigid_Body_Insertions:
579
580----------------------------
581Rigid Body Insertions
582----------------------------
583
584If ``phasedict`` points to the phase information in the data tree, then
585rigid body information is contained in list(s) in
586``phasedict['RBModels']['Residue']`` and/or ``phasedict['RBModels']['Vector']``
587for each rigid body inserted into the current phase.
588
589.. tabularcolumns:: |l|p{4.5in}|
590
591==============   ===================================================================================
592key              explanation
593==============   ===================================================================================
594fixOrig           Should the origin be fixed (when editing, not the refinement flag)
595Ids               Ids for assignment of atoms in the rigid body
596numChain          Chain number for macromolecular fits
597Orient            Orientation of the RB as a quaternion and a refinement flag (' ', 'A' or 'AV')
598OrientVec         Orientation of the RB expressed as a vector and azimuthal rotation angle
599Orig              Origin of the RB in fractional coordinates and refinement flag (bool)
600RBId              References the unique ID of a rigid body in the
601                  :ref:`Rigid Body Objects <RBData_table>`
602RBname            The name for the rigid body (str)
603AtomFrac          The atom fractions for the rigid body
604ThermalMotion     The thermal motion description for the rigid body, which includes a choice for
605                  the model and can include TLS parameters or an overall Uiso value.
606Torsions          Defines the torsion angle and refinement flag for each torsion defined in
607                  the :ref:`Rigid Body Object <RBData_table>`
608==============   ===================================================================================
609
610.. _Powder_table:
611
612.. index::
613   single: Powder data object description
614   single: Data object descriptions; Powder Data
615
616Powder Diffraction Tree Items
617-----------------------------
618
619Every powder diffraction histogram is stored in the GSAS-II data tree
620with a top-level entry named beginning with the string "PWDR ". The
621diffraction data for that information are directly associated with
622that tree item and there are a series of children to that item. The
623routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
624and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
625load this information into a dictionary where the child tree name is
626used as a key, and the information in the main entry is assigned
627a key of ``Data``, as outlined below.
628
629.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
630
631======================     ===============  ===========================================================
632  key                       sub-key          explanation
633======================     ===============  ===========================================================
634Comments                    \\               (list of str) Text strings extracted from the original powder
635                                            data header. These cannot be changed by the user;
636                                            it may be empty.
637Limits                      \\               (list) two two element lists, as [[Ld,Hd],[L,H]]
638                                            where L and Ld are the current and default lowest
639                                            two-theta value to be used and
640                                            where H and Hd are the current and default highest
641                                            two-theta value to be used.
642Reflection Lists            \\               (dict of dicts) with an entry for each phase in the
643                                            histogram. The contents of each dict item
644                                            is a dict containing reflections, as described in
645                                            the :ref:`Powder Reflections <PowderRefl_table>`
646                                            description.
647Instrument Parameters       \\               (dict) The instrument parameters uses different dicts
648                                            for the constant wavelength (CW) and time-of-flight (TOF)
649                                            cases. See below for the descriptions of each.
650wtFactor                    \\               (float) A weighting factor to increase or decrease
651                                            the leverage of data in the histogram .
652                                            A value of 1.0 weights the data with their
653                                            standard uncertainties and a larger value
654                                            increases the weighting of the data (equivalent
655                                            to decreasing the uncertainties).
656Sample Parameters           \\               (dict) Parameters that describe how
657                                            the data were collected, as listed
658                                            below. Refinable parameters are a list containing
659                                            a float and a bool, where the second value
660                                            specifies if the value is refined, otherwise
661                                            the value is a float unless otherwise noted.
662\\                           Scale           The histogram scale factor (refinable)
663\\                           Absorption      The sample absorption coefficient as
664                                            :math:`\\mu r` where r is the radius
665                                            (refinable). Only valid for Debye-Scherrer geometry.
666\\                           SurfaceRoughA   Surface roughness parameter A as defined by
667                                            Surotti, *J. Appl. Cryst*, **5**, 325-331, 1972.
668                                            (refinable - only valid for Bragg-Brentano geometry)
669\\                           SurfaceRoughB   Surface roughness parameter B (refinable -
670                                            only valid for Bragg-Brentano geometry)
671\\                           DisplaceX,      Sample displacement from goniometer center
672                            DisplaceY       where Y is along the beam direction and
673                                            X is perpendicular. Units are :math:`\\mu m`
674                                            (refinable).
675\\                           Phi, Chi,       Goniometer sample setting angles, in degrees.
676                            Omega
677\\                           Gonio. radius   Radius of the diffractometer in mm
678\\                           InstrName       (str) A name for the instrument, used in preparing
679                                            a CIF .
680\\                           Force,          Variables that describe how the measurement
681                            Temperature,    was performed. Not used directly in
682                            Humidity,       any computations.
683                            Pressure,
684                            Voltage
685\\                           ranId           (int) The random-number Id for the histogram
686                                            (same value as where top-level key is ranId)
687\\                           Type            (str) Type of diffraction data, may be 'Debye-Scherrer'
688                                            or 'Bragg-Brentano' .
689hId                         \\               (int) The number assigned to the histogram when
690                                            the project is loaded or edited (can change)
691ranId                       \\               (int) A random number id for the histogram
692                                            that does not change
693Background                  \\               (list) The background is stored as a list with where
694                                            the first item in the list is list and the second
695                                            item is a dict. The list contains the background
696                                            function and its coefficients; the dict contains
697                                            Debye diffuse terms and background peaks.
698                                            (TODO: this needs to be expanded.)
699Data                        \\               (list) The data consist of a list of 6 np.arrays
700                                            containing in order:
701
702                                            0. the x-postions (two-theta in degrees),
703                                            1. the intensity values (Yobs),
704                                            2. the weights for each Yobs value
705                                            3. the computed intensity values (Ycalc)
706                                            4. the background values
707                                            5. Yobs-Ycalc
708======================     ===============  ===========================================================
709
710.. _CWPowder_table:
711
712.. index::
713   single: Powder data CW Instrument Parameters
714
715-----------------------------
716CW Instrument Parameters
717-----------------------------
718
719Instrument Parameters are placed in a list of two dicts,
720where the keys in the first dict are listed below. Note that the dict contents are different for
721constant wavelength (CW) vs. time-of-flight (TOF) histograms.
722The value for each item is a list containing three values: the initial value, the current value
723and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
724cannot be refined. The first and second values are floats unless otherwise noted.
725Items not refined are noted as [*]
726
727.. tabularcolumns:: |l|p{1in}|p{4in}|
728
729========================    ===============  ===========================================================
730  key                       sub-key           explanation
731========================    ===============  ===========================================================
732Instrument Parameters[0]    Type [*]            (str) Histogram type:
733                                                * 'PXC' for constant wavelength x-ray
734                                                * 'PNC' for constant wavelength neutron
735\\                           Bank [*]            (int) Data set number in a multidata file (usually 1)
736\\                           Lam                 (float) Specifies a wavelength in :math:`\\AA`
737\\                           Lam1 [*]            (float) Specifies the primary wavelength in
738                                                :math:`\\AA`, used in place of Lam
739                                                when an :math:`\\alpha_1, \\alpha_2`
740                                                source is used.
741\\                           Lam2 [*]            (float) Specifies the secondary wavelength in
742                                                :math:`\\AA`, used with Lam1
743\\                           I(L2)/I(L1)         (float) Ratio of Lam2 to Lam1, used with Lam1
744\\                           Zero                (float) Two-theta zero correction in *degrees*
745\\                           Azimuth [*]         (float) Azimuthal setting angle for data recorded with differing setting angles
746\\                           U, V, W             (float) Cagliotti profile coefficients
747                                                for Gaussian instrumental broadening, where the
748                                                FWHM goes as
749                                                :math:`U \\tan^2\\theta + V \\tan\\theta + W`
750\\                           X, Y, Z             (float) Cauchy (Lorentzian) instrumental broadening coefficients
751\\                           SH/L                (float) Variant of the Finger-Cox-Jephcoat asymmetric
752                                                peak broadening ratio. Note that this is the
753                                                sum of S/L and H/L where S is
754                                                sample height, H is the slit height and
755                                                L is the goniometer diameter.
756\\                           Polariz.            (float) Polarization coefficient.
757Instrument Parameters[1]                        (empty dict)
758========================    ===============  ===========================================================
759
760.. _TOFPowder_table:
761
762.. index::
763   single: Powder data TOF Instrument Parameters
764
765-----------------------------
766TOF Instrument Parameters
767-----------------------------
768
769Instrument Parameters are also placed in a list of two dicts,
770where the keys in each dict listed below, but here for
771time-of-flight (TOF) histograms.
772The value for each item is a list containing three values: the initial value, the current value
773and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
774cannot be refined. The first and second values are floats unless otherwise noted.
775Items not refined are noted as [*]
776
777.. tabularcolumns:: |l|p{1.5in}|p{4in}|
778
779========================    ===============  ===========================================================
780  key                        sub-key          explanation
781========================    ===============  ===========================================================
782Instrument Parameters[0]    Type [*]            (str) Histogram type:
783                                                * 'PNT' for time of flight neutron
784\\                           Bank                (int) Data set number in a multidata file
785\\                           2-theta [*]         (float) Nominal scattering angle for the detector
786\\                           fltPath [*]         (float) Total flight path source-sample-detector
787\\                           Azimuth [*]         (float) Azimuth angle for detector right hand rotation
788                                                from horizontal away from source
789\\                           difC,difA,          (float) Diffractometer constants for conversion of d-spacing to TOF
790                            difB                in microseconds
791\\                           Zero                (float) Zero point offset (microseconds)
792\\                           alpha               (float) Exponential rise profile coefficients
793\\                           beta-0              (float) Exponential decay profile coefficients
794                            beta-1
795                            beta-q
796\\                           sig-0               (float) Gaussian profile coefficients
797                            sig-1
798                            sig-2
799                            sig-q   
800\\                           X,Y,Z               (float) Lorentzian profile coefficients
801Instrument Parameters[1]    Pdabc               (list of 4 float lists) Originally created for use in gsas as optional tables
802                                                of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation
803                                                from the d-spacing and these tables. The d-true column is apparently unused.
804========================    ===============  ===========================================================
805
806
807.. _PowderRefl_table:
808
809.. index::
810   single: Powder reflection object description
811   single: Data object descriptions; Powder Reflections
812
813Powder Reflection Data Structure
814--------------------------------
815
816For every phase in a histogram, the ``Reflection Lists`` value is a dict
817one element of which is `'RefList'`, which is a np.array containing
818reflections. The columns in that array are documented below.
819
820==========  ====================================================
821  index         explanation
822==========  ====================================================
823 0,1,2          h,k,l (float)
824 3              (int) multiplicity
825 4              (float) d-space, :math:`\\AA`
826 5              (float) pos, two-theta
827 6              (float) sig, Gaussian width
828 7              (float) gam, Lorenzian width
829 8              (float) :math:`F_{obs}^2`
830 9              (float) :math:`F_{calc}^2`
831 10             (float) reflection phase, in degrees
832 11             (float) intensity correction for reflection, this times
833                :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
834 12             (float) Preferred orientation correction
835 13             (float) Transmission (absorption correction)
836 14             (float) Extinction correction
837==========  ====================================================
838
839.. _Xtal_table:
840
841.. index::
842   single: Single Crystal data object description
843   single: Data object descriptions; Single crystal data
844
845Single Crystal Tree Items
846-------------------------
847
848Every single crystal diffraction histogram is stored in the GSAS-II data tree
849with a top-level entry named beginning with the string "HKLF ". The
850diffraction data for that information are directly associated with
851that tree item and there are a series of children to that item. The
852routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
853and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
854load this information into a dictionary where the child tree name is
855used as a key, and the information in the main entry is assigned
856a key of ``Data``, as outlined below.
857
858.. tabularcolumns:: |l|l|p{4in}|
859
860======================  ===============     ====================================================
861  key                      sub-key          explanation
862======================  ===============     ====================================================
863Data                        \\               (dict) that contains the
864                                            reflection table,
865                                            as described in the
866                                            :ref:`Single Crystal Reflections
867                                            <XtalRefl_table>`
868                                            description.
869
870Instrument Parameters       \\               (list) containing two dicts where the possible
871                                            keys in each dict are listed below. The value
872                                            for most items is a list containing two values:
873                                            the initial value, the current value.
874                                            The first and second
875                                            values are floats unless otherwise noted.
876\\                           Lam             (two floats) Specifies a wavelength in :math:`\\AA`
877\\                           Type            (two str values) Histogram type :
878                                            * 'SXC' for constant wavelength x-ray
879                                            * 'SNC' for constant wavelength neutron
880                                            * 'SNT' for time of flight neutron
881\\                           InstrName       (str) A name for the instrument, used in preparing a CIF
882wtFactor                    \\               (float) A weighting factor to increase or decrease
883                                            the leverage of data in the histogram.
884                                            A value of 1.0 weights the data with their
885                                            standard uncertainties and a larger value
886                                            increases the weighting of the data (equivalent
887                                            to decreasing the uncertainties).
888
889hId                         \\               (int) The number assigned to the histogram when
890                                            the project is loaded or edited (can change)
891ranId                       \\               (int) A random number id for the histogram
892                                            that does not change
893======================  ===============     ====================================================
894
895.. _XtalRefl_table:
896
897.. index::
898   single: Single Crystal reflection object description
899   single: Data object descriptions; Single Crystal Reflections
900
901Single Crystal Reflection Data Structure
902----------------------------------------
903
904For every single crystal a histogram, the ``'Data'`` item contains
905the structure factors as an np.array in item `'RefList'`.
906The columns in that array are documented below.
907
908.. tabularcolumns:: |l|p{4in}|
909
910==========  ====================================================
911  index         explanation
912==========  ====================================================
913 0,1,2          (float) h,k,l
914 3              (int) multiplicity
915 4              (float) d-space, :math:`\\AA`
916 5              (float) :math:`F_{obs}^2`
917 6              (float) :math:`\\sigma(F_{obs}^2)`
918 7              (float) :math:`F_{calc}^2`
919 8              (float) :math:`F_{obs}^2T`
920 9              (float) :math:`F_{calc}^2T`
921 10             (float) reflection phase, in degrees
922 11             (float) intensity correction for reflection, this times
923                :math:`F_{obs}^2` or :math:`F_{calc}^2`
924                gives Iobs or Icalc
925==========  ====================================================
926
927.. _Image_table:
928
929.. index::
930   image: Image data object description
931   image: Image object descriptions
932
933Image Data Structure
934--------------------
935
936Every 2-dimensional image is stored in the GSAS-II data tree
937with a top-level entry named beginning with the string "IMG ". The
938image data are directly associated with that tree item and there
939are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
940and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
941load this information into a dictionary where the child tree name is
942used as a key, and the information in the main entry is assigned
943a key of ``Data``, as outlined below.
944
945.. tabularcolumns:: |l|l|p{4in}|
946
947======================  ======================  ====================================================
948  key                      sub-key              explanation
949======================  ======================  ====================================================
950Comments                    \\                   (list of str) Text strings extracted from the original image data
951                                                header or a metafile. These cannot be changed by
952                                                the user; it may be empty.
953Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
954                                                value. Accomodates
955                                                detector orientations other than with the detector
956                                                X-axis
957                                                horizontal.
958\\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
959                                                during image integration multiplied by value. It must have the same size/shape as
960                                                the integrated image. NB: value < 0 for subtraction.
961\\                           calibrant           (str) The material used for determining the position/orientation
962                                                of the image. The data is obtained from :func:`ImageCalibrants`
963                                                and UserCalibrants.py (supplied by user).
964\\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
965\\                           calibskip           (int) The number of expected diffraction lines skipped during the last
966                                                calibration run.
967\\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
968                                                strikes the detector plane as determined by calibration. This point
969                                                does not have to be within the limits of the detector boundaries.
970\\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
971                                                of the image is at the center line otherwise it is at the leading edge.
972\\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
973\\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
974                                                calibration calculations. See pixLimit for details as how point is found.
975\\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
976                                                ring offset at higher angles. Optionally determined by calibration.
977\\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
978\\                           distance            (float) The distance (mm) from sample to detector plane.
979\\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
980                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
981                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
982                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
983                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
984\\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
985\\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
986\\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
987                                                Required for texture calculations.
988\\                           invert_x            (bool) If True display the image with the x-axis inverted.
989\\                           invert_y            (bool) If True display the image with the y-axis inverted.
990\\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
991\\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
992\\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
993                                                intensities obtained during integration.
994\\                           outAzimuths         (int) The number of azimuth pie slices.
995\\                           outChannels         (int) The number of 2-theta steps.
996\\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
997\\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
998                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
999                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
1000                                                Locations are used to construct rings of points for calibration calcualtions.
1001\\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
1002                                                integration using value.
1003\\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
1004                                                diffraction ring with the same d-spacing (dsp)
1005\\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
1006                                                selected by the user,
1007\\                           Range               (list) The minimum & maximum values of the image
1008\\                           rotation            (float) The angle between the x-axis and the vector about which the
1009                                                detector is tilted. Constrained to -180 to 180 deg.
1010\\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
1011                                                calculations.
1012\\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
1013                                                to cause correction to be applied.
1014\\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
1015\\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
1016\\                           showLines           (bool) If True then isplay the integration limits to be used.
1017\\                           size                (list:int) The number of pixels on the image x & y axes
1018\\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
1019\\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
1020\\                           wavelength          (float) The radiation wavelength (:math:`\\AA`) as entered by the user
1021                                                (or someday obtained from the image header).
1022Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
1023                                                to be excluded from integration
1024\\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
1025                                                of which is excluded from recalibration and integration. Only one frame is allowed.
1026\\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
1027                                                from integration.
1028\\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
1029                                                to be excluded from integration.
1030\\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
1031                                                to be excluded from integration.
1032\\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
1033                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
1034\\                           SpotMask            (dict: int & array)
1035                                                'esdMul'(int) number of standard deviations above mean ring intensity to mask
1036                                                'spotMask' (bool array) the spot mask for every pixel in image         
1037
1038Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
1039\\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
1040                                                These will be restricted by space group symmetry; result of strain fit refinement.
1041\\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
1042\\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
1043                                                and are used to determine the strain tensor.
1044                                                The dictionary items are:
1045                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
1046                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
1047                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
1048                                                'Esig': (list: float) Esds for Emat from fitting.
1049                                                'pixLimit': (int) Search range to find highest point on ring for each data point
1050                                                'cutoff': (float) I/Ib cutoff for searching.
1051                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
1052                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
1053                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
1054
1055======================  ======================  ====================================================
1056
1057.. _parmDict_table:
1058
1059.. index::
1060   single: Parameter dictionary
1061
1062Parameter Dictionary
1063-------------------------
1064
1065The parameter dictionary contains all of the variable parameters for the refinement.
1066The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
1067It is prepared in two ways. When loaded from the tree
1068(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
1069:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
1070the values are lists with two elements: ``[value, refine flag]``
1071
1072When loaded from the GPX file (in
1073:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
1074dict is the actual parameter value (usually a float, but sometimes a
1075letter or string flag value (such as I or A for iso/anisotropic).
1076
1077Texture implementation
1078------------------------------
1079
1080There are two different places where texture can be treated in GSAS-II.
1081One is for mitigating the effects of texture in a structural refinement.
1082The other is for texture characterization.
1083
1084For reducing the effect of texture in a structural refinement
1085there are entries labeled preferred orientation in each phase's
1086data tab. Two different approaches can be used for this, the March-Dollase
1087model and spherical harmonics.
1088
1089For the March-Dollase model, one axis in reciprocal space is designated as
1090unique (defaulting to the 001 axis) and reflections are corrected
1091according to the angle they make with this axis depending on
1092the March-Dollase ratio. (If unity, no correction is made).
1093The ratio can be greater than one or less than one depending on if
1094crystallites oriented along the designated axis are
1095overrepresented or underrepresented. For most crystal systems there is an
1096obvious choice for the direction of the unique axis and then only a single
1097term needs to be refined. If the number is close to 1, then the correction
1098is not needed.
1099
1100The second method for reducing the effect of texture in a structural
1101refinement is to create a crystallite orientation probability surface as an
1102expansion in terms spherical harmonic functions. Only functions consistent with
1103cylindrical diffraction suymmetry and having texture symmetry
1104consistent with the Laue class of phase are used and are allowed,
1105so the higher the symmetry the fewer terms that are available for a given spherical harmonics order.
1106To use this correction, select the lowest order that provides
1107refinable terms and perform a refinement. If the texture index remains close to
1108one, then the correction is not needed. If a significant improvement is
1109noted in the profile Rwp, one may wish to see if a higher order expansion
1110gives an even larger improvement.
1111
1112To characterize texture in a material, generally one needs data collected with the
1113sample at multiple orientations or, for TOF, with detectors at multiple
1114locations around the sample. In this case the detector orientation is given in
1115each histogram's Sample Parameters and the sample's orientation is described
1116with the Euler angles specifed on the phase's Texture tab, which is also
1117where the texture type (cylindrical, rolling,...) and the spherical
1118harmonic order is selected. This should not be used with a single dataset and
1119should not be used if the preferred orientations corrections are used.
1120
1121The coordinate system used for texture characterization is defined where
1122the sample coordinates (Psi, gamma) are defined with an instrument coordinate
1123system (I, J, K) such that K is normal to the diffraction plane and J is coincident with the
1124direction of the incident radiation beam toward the source. We further define
1125a standard set of right-handed goniometer eulerian angles (Omega, Chi, Phi) so that Omega and Phi are
1126rotations about K and Chi is a rotation about J when Omega = 0. Finally, as the sample
1127may be mounted so that the sample coordinate system (Is, Js, Ks) does not coincide with
1128the instrument coordinate system (I, J, K), we define three eulerian sample rotation angles
1129(Omega-s, Chi-s, Phi-s) that describe the rotation from (Is, Js, Ks) to (I, J, K). The sample rotation
1130angles are defined so that with the goniometer angles at zero Omega-s and Phi-s are rotations
1131about K and Chi-s is a rotation about J.
1132
1133Three typical examples:
1134    1) Bragg-Brentano laboratory diffractometer: Chi=0
1135    2) Debye-Scherrer counter detector; sample capillary axis perpendicular to diffraction plane: Chi=90
1136    3) Debye-Scherrer 2D area detector positioned directly behind sample; sample capillary axis horizontal; Chi=0
1137            NB: The area detector azimuthal angle = 0 in horizontal plane to right as viewed from x-ray source & 90 at vertical "up" direction
1138           
1139ISODISTORT implementation
1140------------------------------
1141
1142CIFs prepared with the ISODISTORT web site
1143https://stokes.byu.edu/iso/isodistort_version5.6.1/isodistort.php
1144[B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions." J. Appl. Cryst. 39, 607-614 (2006).]
1145can be read into GSAS-II using import CIF. This will cause constraints to be established for structural distortion modes read from the CIF.
1146At present, of the five types of modes  only displacive(``_iso_displacivemode``...) and occupancy (``_iso_occupancymode``...) are processed. Not yet processed: ``_iso_magneticmode``..., ``_iso_rotationalmode``... & ``_iso_strainmode``...
1147
1148The CIF importer :mod:`G2phase_CIF` implements class :class:`G2phase_CIF.CIFPhaseReader` which offers two methods associated with ISODISTORT (ID) input. Method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_test`
1149checks to see if a CIF block contains the loops with ``_iso_displacivemode_label`` or  ``_iso_occupancymode_label`` items.
1150If so, method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_proc` is called to read and interpret them.
1151The results are placed into the reader object's ``.Phase`` class variable as a dict item with key ``'ISODISTORT'``.
1152
1153Note that each mode ID has a long label with a name such as  Pm-3m[1/2,1/2,1/2]R5+(a,a,0)[La:b:dsp]T1u(a). Function :func:`G2phase_CIF.ISODISTORT_shortLbl` is used to create a short name for this,
1154such as R5_T1u(a) which is made unique by addition of _n if the short name is duplicated.
1155As each mode is processed, a constraint corresponding to that mode is
1156created and is added to list in the reader object's ``.Constraints`` class variable. Items placed into that list can either be a list, which corresponds to a function (new var) type :ref:`constraint definition <Constraints_table>` entry, or an item can be a dict, which provides help information for each constraint.
1157
1158------------------------------
1159Displacive modes
1160------------------------------
1161
1162The coordinate variables, as named by ISODISTORT, are placed in
1163``.Phase['ISODISTORT']['IsoVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2VarList']``. The mode variables,
1164as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2ModeList']``.
1165[Use ``str(G2VarObj)`` to get the variable name from the G2VarObj object, but note that the phase number, *n*, for the prefix "*n*::" cannot be determined as the phase number is not yet assigned.]
1166
1167Displacive modes are a bit complex in that they relate to delta displacements, relative to an offset value for each coordinate, and because the modes are normalized, while GSAS-II also uses displacements, but these are added to the coordinates after each refinement cycle and the delta values are set to zero. ISODISTORT uses fixed offsets (subtracted from the actual position to obtain the delta values) that are taken from ``_iso_coordinate_formula`` and these are placed in ``.Phase['ISODISTORT']['ParentStructure]`` (keyed by atom label). The normalization factors (which the delta values are divided by) are taken from ``_iso_displacivemodenorm_value`` and are placed in ``.Phase['ISODISTORT']['NormList']`` in the same order as as ``...['IsoModeList']`` and
1168``...['G2ModeList']``.
1169
1170The CIF contains a sparse matrix, from the ``loop_`` containing
1171``_iso_displacivemodematrix_value`` which provides the equations for determining the mode values from the coordinates, that matrix is placed in ``.Phase['ISODISTORT']['Mode2VarMatrix']``. The matrix is inverted to produce
1172``.Phase['ISODISTORT']['Var2ModeMatrix']``, which determines how to compute the
1173mode values from the delta coordinate values. These values are used for the
1174in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1175values, the latter with s.u. values.
1176
1177
1178------------------------------
1179Occupancy modes
1180------------------------------
1181
1182
1183The delta occupancy variables, as named by ISODISTORT, are placed in
1184``.Phase['ISODISTORT']['OccVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2OccVarList']``. The mode variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['OccModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2OccModeList']``.
1185
1186Occupancy modes, like Displacive modes, are also refined as delta values.  However, GSAS-II directly refines the fractional occupancies.
1187Offset values for each atom, are taken from ``_iso_occupancy_formula`` and are placed in
1188``.Phase['ISODISTORT']['ParentOcc]``.
1189(Offset values are subtracted from the actual position to obtain the delta values.)
1190Modes are normalized (where the mode values are divided by the normalization factor)
1191are taken from ``_iso_occupancymodenorm_value`` and are placed in ``.Phase['ISODISTORT']['OccNormList']`` in the same order as as ``...['OccModeList']`` and
1192``...['G2OccModeList']``.
1193
1194The CIF contains a sparse matrix, from the ``loop_`` containing
1195``_iso_occupancymodematrix_value``, which provides the equations for determining the mode values from the coordinates. That matrix is placed in ``.Phase['ISODISTORT']['Occ2VarMatrix']``. The matrix is inverted to produce
1196``.Phase['ISODISTORT']['Var2OccMatrix']``, which determines how to compute the
1197mode values from the delta coordinate values.
1198
1199
1200------------------------------
1201Mode Computations
1202------------------------------
1203
1204Constraints are processed after the CIF has been read in
1205:meth:`GSASIIdataGUI.GSASII.OnImportPhase` or 
1206:meth:`GSASIIscriptable.G2Project.add_phase` by moving them from the reader
1207object's ``.Constraints`` class variable to
1208the Constraints tree entry's ['Phase'] list (for list items defining constraints) or
1209the Constraints tree entry's ['_Explain'] dict (for dict items defining constraint help information)
1210
1211The information in ``.Phase['ISODISTORT']`` is used
1212in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1213values, the latter with s.u. values. This can be called from the Constraints and Phase/Atoms tree items.
1214
1215Before each refinement, constraints are processed as
1216:ref:`described elsewhere <Constraints_processing>`. After a refinement
1217is complete, :func:`GSASIImapvars.PrintIndependentVars` shows the
1218shifts and s.u.'s on the refined modes, using GSAS-II values, but
1219:func:`GSASIIstrIO.PrintISOmodes` prints the ISODISTORT modes as computed
1220in the web site.
1221
1222
1223.. _ParameterLimits:
1224
1225.. index::
1226   single: Parameter limits
1227
1228Parameter Limits
1229------------------------------
1230
1231One of the most often requested "enhancements" for GSAS-II would be the inclusion
1232of constraints to force parameters such as occupancies or Uiso values to stay within
1233expected ranges. While it is possible for users to supply their own restraints that would
1234perform this by supplying an appropriate expression with the "General" restraints, the
1235GSAS-II authors do not feel that use of restraints or constraints are a good solution for
1236this common problem where parameters refine to non-physical values. This is because when
1237this occurs, most likely one of the following cases is occurring:
1238
1239#. there is a significant problem
1240   with the model, for example for an x-ray fit if an O atom is placed where a S is actually
1241   present, the Uiso will refine artificially small or the occupancy much larger than unity
1242   to try to compensate for the missing electrons; or
1243 
1244#. the data are simply insensitive
1245   to the parameter or combination of parameters, for example unless very high-Q data
1246   are included, the effects of a occupancy and Uiso value can have compensating effects,
1247   so an assumption must be made; likewise, with neutron data natural-abundance V atoms
1248   are nearly invisible due to weak coherent scattering. No parameters can be fit for a
1249   V atom with neutrons.
1250
1251#. the parameter is non-physical (such as a negative Uiso value) but within
1252   two sigma (sigma = standard uncertainty, aka e.s.d.) of a reasonable value,
1253   in which case the
1254   value is not problematic as it is experimentally indistinguishable from an
1255   expected value. 
1256
1257#. there is a systematic problem with the data (experimental error)
1258
1259In all these cases, this situation needs to be reviewed by a crystallographer to decide
1260how to best determine a structural model for these data. An implementation with a constraint
1261or restraint is likely to simply hide the problem from the user, making it more probable
1262that a poor model choice is obtained.
1263
1264What GSAS-II does implement is to allow users to specify ranges for parameters
1265that works by disabling
1266refinement of parameters that refine beyond either a lower limit or an upper limit, where
1267either or both may be optionally specified. Parameters limits are specified in the Controls
1268tree entry in dicts named as ``Controls['parmMaxDict']`` and ``Controls['parmMinDict']``, where
1269the keys are :class:`G2VarObj` objects corresponding to standard GSAS-II variable
1270(see :func:`getVarDescr` and :func:`CompileVarDesc`) names, where a
1271wildcard ('*') may optionally be used for histogram number or atom number
1272(phase number is intentionally not  allowed as a wildcard as it makes little sense
1273to group the same parameter together different phases). Note
1274that :func:`prmLookup` is used to see if a name matches a wildcard. The upper or lower limit
1275is placed into these dicts as a float value. These values can be edited using the window
1276created by the Calculate/"View LS parms" menu command or in scripting with the
1277:meth:`GSASIIscriptable.G2Project.set_Controls` function.
1278In the GUI, a checkbox labeled "match all histograms/atoms" is used to insert a wildcard
1279into the appropriate part of the variable name.
1280
1281When a refinement is conducted, routine :func:`GSASIIstrMain.dropOOBvars` is used to
1282find parameters that have refined to values outside their limits. If this occurs, the parameter
1283is set to the limiting value and the variable name is added to a list of frozen variables
1284(as a :class:`G2VarObj` objects) kept in a list in the
1285``Controls['parmFrozen']`` dict. In a sequential refinement, this is kept separate for
1286each histogram as a list in
1287``Controls['parmFrozen'][histogram]`` (where the key is the histogram name) or as a list in
1288``Controls['parmFrozen']['FrozenList']`` for a non-sequential fit.
1289This allows different variables
1290to be frozen in each section of a sequential fit.
1291Frozen parameters are not included in refinements through removal from the
1292list of parameters to be refined (``varyList``) in :func:`GSASIIstrMain.Refine` or
1293:func:`GSASIIstrMain.SeqRefine`.
1294The data window for the Controls tree item shows the number of Frozen variables and
1295the individual variables can be viewed with the Calculate/"View LS parms" menu window or
1296obtained with :meth:`GSASIIscriptable.G2Project.get_Frozen`.
1297Once a variable is frozen, it will not be refined in any
1298future refinements unless the the variable is removed (manually) from the list. This can also
1299be done with the Calculate/"View LS parms" menu window or
1300:meth:`GSASIIscriptable.G2Project.set_Frozen`.
1301
1302
1303.. seealso::
1304  :class:`G2VarObj`
1305  :func:`getVarDescr`
1306  :func:`CompileVarDesc`
1307  :func:`prmLookup`
1308  :class:`GSASIIctrlGUI.ShowLSParms`
1309  :class:`GSASIIctrlGUI.VirtualVarBox`
1310  :func:`GSASIIstrIO.SetUsedHistogramsAndPhases`
1311  :func:`GSASIIstrIO.SaveUpdatedHistogramsAndPhases`
1312  :func:`GSASIIstrIO.SetSeqResult`
1313  :func:`GSASIIstrMain.dropOOBvars`
1314  :meth:`GSASIIscriptable.G2Project.set_Controls`
1315  :meth:`GSASIIscriptable.G2Project.get_Frozen`
1316  :meth:`GSASIIscriptable.G2Project.set_Frozen`
1317
1318*Classes and routines*
1319----------------------
1320
1321'''
1322from __future__ import division, print_function
1323import platform
1324import re
1325import random as ran
1326import sys
1327import os.path as ospath
1328if '2' in platform.python_version_tuple()[0]:
1329    import cPickle
1330else:
1331    import pickle as cPickle
1332import GSASIIpath
1333import GSASIImath as G2mth
1334import GSASIIspc as G2spc
1335import numpy as np
1336
1337GSASIIpath.SetVersionNumber("$Revision: 4960 $")
1338
1339DefaultControls = {
1340    'deriv type':'analytic Hessian',
1341    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
1342    'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
1343    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
1344    'Author':'no name',
1345    'FreePrm1':'Sample humidity (%)',
1346    'FreePrm2':'Sample voltage (V)',
1347    'FreePrm3':'Applied load (MN)',
1348    'ShowCell':False,
1349    }
1350'''Values to be used as defaults for the initial contents of the ``Controls``
1351data tree item.
1352'''
1353def StripUnicode(string,subs='.'):
1354    '''Strip non-ASCII characters from strings
1355
1356    :param str string: string to strip Unicode characters from
1357    :param str subs: character(s) to place into string in place of each
1358      Unicode character. Defaults to '.'
1359
1360    :returns: a new string with only ASCII characters
1361    '''
1362    s = ''
1363    for c in string:
1364        if ord(c) < 128:
1365            s += c
1366        else:
1367            s += subs
1368    return s
1369#    return s.encode('ascii','replace')
1370
1371def MakeUniqueLabel(lbl,labellist):
1372    '''Make sure that every a label is unique against a list by adding
1373    digits at the end until it is not found in list.
1374
1375    :param str lbl: the input label
1376    :param list labellist: the labels that have already been encountered
1377    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
1378      ``_10-99``, etc.) appended at the end
1379    '''
1380    lbl = StripUnicode(lbl.strip(),'_')
1381    if not lbl: # deal with a blank label
1382        lbl = '_1'
1383    if lbl not in labellist:
1384        labellist.append(lbl)
1385        return lbl
1386    i = 1
1387    prefix = lbl
1388    if '_' in lbl:
1389        prefix = lbl[:lbl.rfind('_')]
1390        suffix = lbl[lbl.rfind('_')+1:]
1391        try:
1392            i = int(suffix)+1
1393        except: # suffix could not be parsed
1394            i = 1
1395            prefix = lbl
1396    while prefix+'_'+str(i) in labellist:
1397        i += 1
1398    else:
1399        lbl = prefix+'_'+str(i)
1400        labellist.append(lbl)
1401    return lbl
1402
1403PhaseIdLookup = {}
1404'''dict listing phase name and random Id keyed by sequential phase index as a str;
1405best to access this using :func:`LookupPhaseName`
1406'''
1407PhaseRanIdLookup = {}
1408'''dict listing phase sequential index keyed by phase random Id;
1409best to access this using :func:`LookupPhaseId`
1410'''
1411HistIdLookup = {}
1412'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
1413best to access this using :func:`LookupHistName`
1414'''
1415HistRanIdLookup = {}
1416'''dict listing histogram sequential index keyed by histogram random Id;
1417best to access this using :func:`LookupHistId`
1418'''
1419AtomIdLookup = {}
1420'''dict listing for each phase index as a str, the atom label and atom random Id,
1421keyed by atom sequential index as a str;
1422best to access this using :func:`LookupAtomLabel`
1423'''
1424AtomRanIdLookup = {}
1425'''dict listing for each phase the atom sequential index keyed by atom random Id;
1426best to access this using :func:`LookupAtomId`
1427'''
1428ShortPhaseNames = {}
1429'''a dict containing a possibly shortened and when non-unique numbered
1430version of the phase name. Keyed by the phase sequential index.
1431'''
1432ShortHistNames = {}
1433'''a dict containing a possibly shortened and when non-unique numbered
1434version of the histogram name. Keyed by the histogram sequential index.
1435'''
1436
1437#VarDesc = {}  # removed 1/30/19 BHT as no longer needed (I think)
1438#''' This dictionary lists descriptions for GSAS-II variables,
1439#as set in :func:`CompileVarDesc`. See that function for a description
1440#for how keys and values are written.
1441#'''
1442
1443reVarDesc = {}
1444''' This dictionary lists descriptions for GSAS-II variables where
1445keys are compiled regular expressions that will match the name portion
1446of a parameter name. Initialized in :func:`CompileVarDesc`.
1447'''
1448
1449reVarStep = {}
1450''' This dictionary lists the preferred step size for numerical
1451derivative computation w/r to a GSAS-II variable. Keys are compiled
1452regular expressions and values are the step size for that parameter.
1453Initialized in :func:`CompileVarDesc`.
1454'''
1455# create a default space group object for P1; N.B. fails when building documentation
1456try:
1457    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1458except:
1459    pass
1460
1461def GetPhaseNames(fl):
1462    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1463    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1464
1465    :param file fl: opened .gpx file
1466    :return: list of phase names
1467    '''
1468    PhaseNames = []
1469    while True:
1470        try:
1471            data = cPickle.load(fl)
1472        except EOFError:
1473            break
1474        datum = data[0]
1475        if 'Phases' == datum[0]:
1476            for datus in data[1:]:
1477                PhaseNames.append(datus[0])
1478    fl.seek(0)          #reposition file
1479    return PhaseNames
1480
1481def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1482    '''Create a new phase dict with default values for various parameters
1483
1484    :param str Name: Name for new Phase
1485
1486    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1487      defaults to data for P 1
1488
1489    :param list cell: unit cell parameter list; defaults to
1490      [1.0,1.0,1.0,90.,90,90.,1.]
1491
1492    '''
1493    if SGData is None: SGData = P1SGData
1494    if cell is None: cell=[1.0,1.0,1.0,90.,90.,90.,1.]
1495    phaseData = {
1496        'ranId':ran.randint(0,sys.maxsize),
1497        'General':{
1498            'Name':Name,
1499            'Type':'nuclear',
1500            'Modulated':False,
1501            'AtomPtrs':[3,1,7,9],
1502            'SGData':SGData,
1503            'Cell':[False,]+cell,
1504            'Pawley dmin':1.0,
1505            'Data plot type':'None',
1506            'SH Texture':{
1507                'Order':0,
1508                'Model':'cylindrical',
1509                'Sample omega':[False,0.0],
1510                'Sample chi':[False,0.0],
1511                'Sample phi':[False,0.0],
1512                'SH Coeff':[False,{}],
1513                'SHShow':False,
1514                'PFhkl':[0,0,1],
1515                'PFxyz':[0,0,1],
1516                'PlotType':'Pole figure',
1517                'Penalty':[['',],0.1,False,1.0]}},
1518        'Atoms':[],
1519        'Drawing':{},
1520        'Histograms':{},
1521        'Pawley ref':[],
1522        'RBModels':{},
1523        }
1524    if Super and Super.get('Use',False):
1525        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1526        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])[1]
1527        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1528
1529    return phaseData
1530
1531def ReadCIF(URLorFile):
1532    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1533    (from James Hester).
1534    The open routine gets confused with DOS names that begin with a letter and colon
1535    "C:\\dir\" so this routine will try to open the passed name as a file and if that
1536    fails, try it as a URL
1537
1538    :param str URLorFile: string containing a URL or a file name. Code will try first
1539      to open it as a file and then as a URL.
1540
1541    :returns: a PyCifRW CIF object.
1542    '''
1543    import CifFile as cif # PyCifRW from James Hester
1544
1545    # alternate approach:
1546    #import urllib
1547    #ciffile = 'file:'+urllib.pathname2url(filename)
1548
1549    try:
1550        fp = open(URLorFile,'r')
1551        cf = cif.ReadCif(fp)
1552        fp.close()
1553        return cf
1554    except IOError:
1555        return cif.ReadCif(URLorFile)
1556
1557def TestIndexAll():
1558    '''Test if :func:`IndexAllIds` has been called to index all phases and
1559    histograms (this is needed before :func:`G2VarObj` can be used.
1560
1561    :returns: Returns True if indexing is needed.
1562    '''
1563    if PhaseIdLookup or AtomIdLookup or HistIdLookup:
1564        return False
1565    return True
1566       
1567def IndexAllIds(Histograms,Phases):
1568    '''Scan through the used phases & histograms and create an index
1569    to the random numbers of phases, histograms and atoms. While doing this,
1570    confirm that assigned random numbers are unique -- just in case lightning
1571    strikes twice in the same place.
1572
1573    Note: this code assumes that the atom random Id (ranId) is the last
1574    element each atom record.
1575
1576    This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
1577    (which loads the histograms and phases from a GPX file),
1578    :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
1579    (which loads the histograms and phases from the data tree.) and
1580    :meth:`GSASIIconstrGUI.UpdateConstraints`
1581    (which displays & edits the constraints in a GUI)
1582
1583    TODO: do we need a lookup for rigid body variables?
1584    '''
1585    # process phases and atoms
1586    PhaseIdLookup.clear()
1587    PhaseRanIdLookup.clear()
1588    AtomIdLookup.clear()
1589    AtomRanIdLookup.clear()
1590    ShortPhaseNames.clear()
1591    for ph in Phases:
1592        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1593        ranId = Phases[ph]['ranId']
1594        while ranId in PhaseRanIdLookup:
1595            # Found duplicate random Id! note and reassign
1596            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1597            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1598        pId = str(Phases[ph]['pId'])
1599        PhaseIdLookup[pId] = (ph,ranId)
1600        PhaseRanIdLookup[ranId] = pId
1601        shortname = ph  #[:10]
1602        while shortname in ShortPhaseNames.values():
1603            shortname = ph[:8] + ' ('+ pId + ')'
1604        ShortPhaseNames[pId] = shortname
1605        AtomIdLookup[pId] = {}
1606        AtomRanIdLookup[pId] = {}
1607        for iatm,at in enumerate(Phases[ph]['Atoms']):
1608            ranId = at[cia+8]
1609            while ranId in AtomRanIdLookup[pId]: # check for dups
1610                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1611                at[cia+8] = ranId = ran.randint(0,sys.maxsize)
1612            AtomRanIdLookup[pId][ranId] = str(iatm)
1613            if Phases[ph]['General']['Type'] == 'macromolecular':
1614                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1615            else:
1616                label = at[ct-1]
1617            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1618    # process histograms
1619    HistIdLookup.clear()
1620    HistRanIdLookup.clear()
1621    ShortHistNames.clear()
1622    for hist in Histograms:
1623        ranId = Histograms[hist]['ranId']
1624        while ranId in HistRanIdLookup:
1625            # Found duplicate random Id! note and reassign
1626            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1627            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1628        hId = str(Histograms[hist]['hId'])
1629        HistIdLookup[hId] = (hist,ranId)
1630        HistRanIdLookup[ranId] = hId
1631        shortname = hist[:15]
1632        while shortname in ShortHistNames.values():
1633            shortname = hist[:11] + ' ('+ hId + ')'
1634        ShortHistNames[hId] = shortname
1635
1636def LookupAtomId(pId,ranId):
1637    '''Get the atom number from a phase and atom random Id
1638
1639    :param int/str pId: the sequential number of the phase
1640    :param int ranId: the random Id assigned to an atom
1641
1642    :returns: the index number of the atom (str)
1643    '''
1644    if not AtomRanIdLookup:
1645        raise Exception('Error: LookupAtomId called before IndexAllIds was run')
1646    if pId is None or pId == '':
1647        raise KeyError('Error: phase is invalid (None or blank)')
1648    pId = str(pId)
1649    if pId not in AtomRanIdLookup:
1650        raise KeyError('Error: LookupAtomId does not have phase '+pId)
1651    if ranId not in AtomRanIdLookup[pId]:
1652        raise KeyError('Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']')
1653    return AtomRanIdLookup[pId][ranId]
1654
1655def LookupAtomLabel(pId,index):
1656    '''Get the atom label from a phase and atom index number
1657
1658    :param int/str pId: the sequential number of the phase
1659    :param int index: the index of the atom in the list of atoms
1660
1661    :returns: the label for the atom (str) and the random Id of the atom (int)
1662    '''
1663    if not AtomIdLookup:
1664        raise Exception('Error: LookupAtomLabel called before IndexAllIds was run')
1665    if pId is None or pId == '':
1666        raise KeyError('Error: phase is invalid (None or blank)')
1667    pId = str(pId)
1668    if pId not in AtomIdLookup:
1669        raise KeyError('Error: LookupAtomLabel does not have phase '+pId)
1670    if index not in AtomIdLookup[pId]:
1671        raise KeyError('Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']')
1672    return AtomIdLookup[pId][index]
1673
1674def LookupPhaseId(ranId):
1675    '''Get the phase number and name from a phase random Id
1676
1677    :param int ranId: the random Id assigned to a phase
1678    :returns: the sequential Id (pId) number for the phase (str)
1679    '''
1680    if not PhaseRanIdLookup:
1681        raise Exception('Error: LookupPhaseId called before IndexAllIds was run')
1682    if ranId not in PhaseRanIdLookup:
1683        raise KeyError('Error: LookupPhaseId does not have ranId '+str(ranId))
1684    return PhaseRanIdLookup[ranId]
1685
1686def LookupPhaseName(pId):
1687    '''Get the phase number and name from a phase Id
1688
1689    :param int/str pId: the sequential assigned to a phase
1690    :returns:  (phase,ranId) where phase is the name of the phase (str)
1691      and ranId is the random # id for the phase (int)
1692    '''
1693    if not PhaseIdLookup:
1694        raise Exception('Error: LookupPhaseName called before IndexAllIds was run')
1695    if pId is None or pId == '':
1696        raise KeyError('Error: phase is invalid (None or blank)')
1697    pId = str(pId)
1698    if pId not in PhaseIdLookup:
1699        raise KeyError('Error: LookupPhaseName does not have index '+pId)
1700    return PhaseIdLookup[pId]
1701
1702def LookupHistId(ranId):
1703    '''Get the histogram number and name from a histogram random Id
1704
1705    :param int ranId: the random Id assigned to a histogram
1706    :returns: the sequential Id (hId) number for the histogram (str)
1707    '''
1708    if not HistRanIdLookup:
1709        raise Exception('Error: LookupHistId called before IndexAllIds was run')
1710    if ranId not in HistRanIdLookup:
1711        raise KeyError('Error: LookupHistId does not have ranId '+str(ranId))
1712    return HistRanIdLookup[ranId]
1713
1714def LookupHistName(hId):
1715    '''Get the histogram number and name from a histogram Id
1716
1717    :param int/str hId: the sequential assigned to a histogram
1718    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1719      and ranId is the random # id for the histogram (int)
1720    '''
1721    if not HistIdLookup:
1722        raise Exception('Error: LookupHistName called before IndexAllIds was run')
1723    if hId is None or hId == '':
1724        raise KeyError('Error: histogram is invalid (None or blank)')
1725    hId = str(hId)
1726    if hId not in HistIdLookup:
1727        raise KeyError('Error: LookupHistName does not have index '+hId)
1728    return HistIdLookup[hId]
1729
1730def fmtVarDescr(varname):
1731    '''Return a string with a more complete description for a GSAS-II variable
1732
1733    :param str varname: A full G2 variable name with 2 or 3 or 4
1734       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1735
1736    :returns: a string with the description
1737    '''
1738    s,l = VarDescr(varname)
1739    return s+": "+l
1740
1741def VarDescr(varname):
1742    '''Return two strings with a more complete description for a GSAS-II variable
1743
1744    :param str name: A full G2 variable name with 2 or 3 or 4
1745       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1746
1747    :returns: (loc,meaning) where loc describes what item the variable is mapped
1748      (phase, histogram, etc.) and meaning describes what the variable does.
1749    '''
1750
1751    # special handling for parameter names without a colon
1752    # for now, assume self-defining
1753    if varname.find(':') == -1:
1754        return "Global",varname
1755
1756    l = getVarDescr(varname)
1757    if not l:
1758        return ("invalid variable name ("+str(varname)+")!"),""
1759#        return "invalid variable name!",""
1760
1761    if not l[-1]:
1762        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1763
1764    if len(l) == 3:         #SASD variable name!
1765        s = 'component:'+l[1]
1766        return s,l[-1]
1767    s = ""
1768    if l[0] is not None and l[1] is not None: # HAP: keep short
1769        if l[2] == "Scale": # fix up ambigous name
1770            l[5] = "Phase fraction"
1771        if l[0] == '*':
1772            lbl = 'Seq. ref.'
1773        else:
1774            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1775        if l[1] == '*':
1776            hlbl = 'Seq. ref.'
1777        else:
1778            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1779        if hlbl[:4] == 'HKLF':
1780            hlbl = 'Xtl='+hlbl[5:]
1781        elif hlbl[:4] == 'PWDR':
1782            hlbl = 'Pwd='+hlbl[5:]
1783        else:
1784            hlbl = 'Hist='+hlbl
1785        s = "Ph="+str(lbl)+" * "+str(hlbl)
1786    else:
1787        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1788            l[5] = "Scale factor"
1789        if l[2] == 'Back': # background parameters are "special", alas
1790            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1791            l[-1] += ' #'+str(l[3])
1792        elif l[4] is not None: # rigid body parameter or modulation parm
1793            lbl = ShortPhaseNames.get(l[0],'phase?')
1794            if 'RB' in l[2]:    #rigid body parm
1795                s = "RB body #"+str(l[3])+" (type "+str(l[4])+") in "+str(lbl) + ','
1796            else: #modulation parm
1797                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1798        elif l[3] is not None: # atom parameter,
1799            lbl = ShortPhaseNames.get(l[0],'phase?')
1800            try:
1801                albl = LookupAtomLabel(l[0],l[3])[0]
1802            except KeyError:
1803                albl = 'Atom?'
1804            s = "Atom "+str(albl)+" in "+str(lbl)
1805        elif l[0] == '*':
1806            s = "All phases "
1807        elif l[0] is not None:
1808            lbl = ShortPhaseNames.get(l[0],'phase?')
1809            s = "Phase "+str(lbl)
1810        elif l[1] == '*':
1811            s = 'All hists'
1812        elif l[1] is not None:
1813            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1814            if hlbl[:4] == 'HKLF':
1815                hlbl = 'Xtl='+hlbl[5:]
1816            elif hlbl[:4] == 'PWDR':
1817                hlbl = 'Pwd='+hlbl[5:]
1818            else:
1819                hlbl = 'Hist='+hlbl
1820            s = str(hlbl)
1821    if not s:
1822        s = 'Global'
1823    return s,l[-1]
1824
1825def getVarDescr(varname):
1826    '''Return a short description for a GSAS-II variable
1827
1828    :param str name: A full G2 variable name with 2 or 3 or 4
1829       colons (<p>:<h>:name[:<a1>][:<a2>])
1830
1831    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1832      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1833      the histogram number and the atom number; `name` will always be
1834      a str; and `description` is str or `None`.
1835      If the variable name is incorrectly formed (for example, wrong
1836      number of colons), `None` is returned instead of a list.
1837    '''
1838    l = varname.split(':')
1839    if len(l) == 2:     #SASD parameter name
1840        return varname,l[0],getDescr(l[1])
1841    if len(l) == 3:
1842        l += [None,None]
1843    elif len(l) == 4:
1844        l += [None]
1845    elif len(l) != 5:
1846        return None
1847    for i in (0,1,3,4):
1848        if l[i] == "":
1849            l[i] = None
1850    l += [getDescr(l[2])]
1851    return l
1852
1853def CompileVarDesc():
1854    '''Set the values in the variable lookup tables
1855    (:attr:`reVarDesc` and :attr:`reVarStep`).
1856    This is called in :func:`getDescr` and :func:`getVarStep` so this
1857    initialization is always done before use.
1858
1859    Note that keys may contain regular expressions, where '[xyz]'
1860    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range
1861    of values). '.*' matches any string. For example::
1862
1863    'AUiso':'Atomic isotropic displacement parameter',
1864
1865    will match variable ``'p::AUiso:a'``.
1866    If parentheses are used in the key, the contents of those parentheses can be
1867    used in the value, such as::
1868
1869    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1870
1871    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1872    in the value when used.
1873
1874    '''
1875    if reVarDesc: return # already done
1876    for key,value in {
1877        # derived or other sequential vars
1878        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1879        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1880        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1881        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1882        # ambiguous, alas:
1883        'Scale' : 'Phase or Histogram scale factor',
1884        # Phase vars (p::<var>)
1885        'A([0-5])' : ('Reciprocal metric tensor component \\1',1e-5),
1886        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1887        # Atom vars (p::<var>:a)
1888        'dA([xyz])$' : ('change to atomic coordinate, \\1',1e-6),
1889        'A([xyz])$' : '\\1 fractional atomic coordinate',
1890        'AUiso':('Atomic isotropic displacement parameter',1e-4),
1891        'AU([123][123])':('Atomic anisotropic displacement parameter U\\1',1e-4),
1892        'Afrac': ('Atomic site fraction parameter',1e-5),
1893        'Amul': 'Atomic site multiplicity value',
1894        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1895        # Hist (:h:<var>) & Phase (HAP) vars (p:h:<var>)
1896        'Back': 'Background term',
1897        'BkPkint;(.*)':'Background peak #\\1 intensity',
1898        'BkPkpos;(.*)':'Background peak #\\1 position',
1899        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1900        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1901#        'Back File' : 'Background file name',
1902        'BF mult' : 'Background file multiplier',
1903        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1904        'D([123][123])' : 'Anisotropic strain coef. \\1',
1905        'Extinction' : 'Extinction coef.',
1906        'MD' : 'March-Dollase coef.',
1907        'Mustrain;.*' : 'Microstrain coef.',
1908        'Size;.*' : 'Crystallite size value',
1909        'eA$' : 'Cubic mustrain value',
1910        'Ep$' : 'Primary extinction',
1911        'Es$' : 'Secondary type II extinction',
1912        'Eg$' : 'Secondary type I extinction',
1913        'Flack' : 'Flack parameter',
1914        'TwinFr' : 'Twin fraction',
1915        'Layer Disp'  : 'Layer displacement along beam',
1916        #Histogram vars (:h:<var>)
1917        'Absorption' : 'Absorption coef.',
1918        'Displace([XY])' : ('Debye-Scherrer sample displacement \\1',0.1),
1919        'Lam' : ('Wavelength',1e-6),
1920        'I\\(L2\\)\\/I\\(L1\\)' : ('Ka2/Ka1 intensity ratio',0.001),
1921        'Polariz\\.' : ('Polarization correction',1e-3),
1922        'SH/L' : ('FCJ peak asymmetry correction',1e-4),
1923        '([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),
1924        '([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),
1925        'Zero' : 'Debye-Scherrer zero correction',
1926        'Shift' : 'Bragg-Brentano sample displ.',
1927        'SurfRoughA' : 'Bragg-Brenano surface roughness A',
1928        'SurfRoughB' : 'Bragg-Brenano surface roughness B',
1929        'Transparency' : 'Bragg-Brentano sample tranparency',
1930        'DebyeA' : 'Debye model amplitude',
1931        'DebyeR' : 'Debye model radius',
1932        'DebyeU' : 'Debye model Uiso',
1933        'RBV.*' : 'Vector rigid body parameter',
1934        'RBVO([aijk])' : 'Vector rigid body orientation parameter \\1',
1935        'RBVP([xyz])' : 'Vector rigid body \\1 position parameter',
1936        'RBVf' : 'Vector rigid body site fraction',
1937        'RBV([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1938        'RBVU' : 'Residue rigid body group Uiso param.',
1939        'RBRO([aijk])' : 'Residue rigid body orientation parameter \\1',
1940        'RBRP([xyz])' : 'Residue rigid body \\1 position parameter',
1941        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1942        'RBRf' : 'Residue rigid body site fraction',
1943        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1944        'RBRU' : 'Residue rigid body group Uiso param.',
1945        'constr([0-9]*)' : 'Parameter from constraint',
1946        'nv-([^_]+)_*' : 'New variable constraint parameter named \\1',
1947        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1948        'mV([0-2])$' : 'Modulation vector component \\1',
1949        'Fsin'  :   'Sin site fraction modulation',
1950        'Fcos'  :   'Cos site fraction modulation',
1951        'Fzero'  :   'Crenel function offset',      #may go away
1952        'Fwid'   :   'Crenel function width',
1953        'Tmin'   :   'ZigZag/Block min location',
1954        'Tmax'   :   'ZigZag/Block max location',
1955        '([XYZ])max': 'ZigZag/Block max value for \\1',
1956        '([XYZ])sin'  : 'Sin position wave for \\1',
1957        '([XYZ])cos'  : 'Cos position wave for \\1',
1958        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1959        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1960        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1961        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1962        # PDF peak parms (l:<var>;l = peak no.)
1963        'PDFpos'  : 'PDF peak position',
1964        'PDFmag'  : 'PDF peak magnitude',
1965        'PDFsig'  : 'PDF peak std. dev.',
1966        # SASD vars (l:<var>;l = component)
1967        'Aspect ratio' : 'Particle aspect ratio',
1968        'Length' : 'Cylinder length',
1969        'Diameter' : 'Cylinder/disk diameter',
1970        'Thickness' : 'Disk thickness',
1971        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1972        'Dist' : 'Interparticle distance',
1973        'VolFr' : 'Dense scatterer volume fraction',
1974        'epis' : 'Sticky sphere epsilon',
1975        'Sticky' : 'Stickyness',
1976        'Depth' : 'Well depth',
1977        'Width' : 'Well width',
1978        'Volume' : 'Particle volume',
1979        'Radius' : 'Sphere/cylinder/disk radius',
1980        'Mean' : 'Particle mean radius',
1981        'StdDev' : 'Standard deviation in Mean',
1982        'G$': 'Guinier prefactor',
1983        'Rg$': 'Guinier radius of gyration',
1984        'B$': 'Porod prefactor',
1985        'P$': 'Porod power',
1986        'Cutoff': 'Porod cutoff',
1987        'PkInt': 'Bragg peak intensity',
1988        'PkPos': 'Bragg peak position',
1989        'PkSig': 'Bragg peak sigma',
1990        'PkGam': 'Bragg peak gamma',
1991        'e([12][12])' : 'strain tensor e\\1',   # strain vars e11, e22, e12
1992        'Dcalc': 'Calc. d-spacing',
1993        'Back$': 'background parameter',
1994        'pos$': 'peak position',
1995        'int$': 'peak intensity',
1996        'WgtFrac':'phase weight fraction',
1997        'alpha':'TOF profile term',
1998        'alpha-[01]':'Pink profile term',
1999        'beta-[01q]':'TOF/Pink profile term',
2000        'sig-[012q]':'TOF profile term',
2001        'dif[ABC]':'TOF to d-space calibration',
2002        'C\\([0-9]*,[0-9]*\\)' : 'spherical harmonics preferred orientation coef.',
2003        'Pressure': 'Pressure level for measurement in MPa',
2004        'Temperature': 'T value for measurement, K',
2005        'FreePrm([123])': 'User defined measurement parameter \\1',
2006        'Gonio. radius': 'Distance from sample to detector, mm',
2007        }.items():
2008        # Needs documentation: HAP: LayerDisp, LeBail, newLeBail
2009        # hist: Azimuth, Chi, Omega, Phi, Bank, nDebye, nPeaks
2010       
2011        if len(value) == 2:
2012            #VarDesc[key] = value[0]
2013            reVarDesc[re.compile(key)] = value[0]
2014            reVarStep[re.compile(key)] = value[1]
2015        else:
2016            #VarDesc[key] = value
2017            reVarDesc[re.compile(key)] = value
2018
2019def removeNonRefined(parmList):
2020    '''Remove items from variable list that are not refined and should not
2021    appear as options for constraints
2022
2023    :param list parmList: a list of strings of form "p:h:VAR:a" where
2024      VAR is the variable name
2025
2026    :returns: a list after removing variables where VAR matches a
2027      entry in local variable NonRefinedList
2028    '''
2029    NonRefinedList = ['Omega','Type','Chi','Phi', 'Azimuth','Gonio. radius',
2030                          'Lam1','Lam2','Back','Temperature','Pressure',
2031                          'FreePrm1','FreePrm2','FreePrm3',
2032                          'Source','nPeaks','LeBail','newLeBail','Bank',
2033                          'nDebye', #'',
2034                    ]
2035    return [prm for prm in parmList if prm.split(':')[2] not in NonRefinedList]
2036       
2037def getDescr(name):
2038    '''Return a short description for a GSAS-II variable
2039
2040    :param str name: The descriptive part of the variable name without colons (:)
2041
2042    :returns: a short description or None if not found
2043    '''
2044
2045    CompileVarDesc() # compile the regular expressions, if needed
2046    for key in reVarDesc:
2047        m = key.match(name)
2048        if m:
2049            reVarDesc[key]
2050            return m.expand(reVarDesc[key])
2051    return None
2052
2053def getVarStep(name,parmDict=None):
2054    '''Return a step size for computing the derivative of a GSAS-II variable
2055
2056    :param str name: A complete variable name (with colons, :)
2057    :param dict parmDict: A dict with parameter values or None (default)
2058
2059    :returns: a float that should be an appropriate step size, either from
2060      the value supplied in :func:`CompileVarDesc` or based on the value for
2061      name in parmDict, if supplied. If not found or the value is zero,
2062      a default value of 1e-5 is used. If parmDict is None (default) and
2063      no value is provided in :func:`CompileVarDesc`, then None is returned.
2064    '''
2065    CompileVarDesc() # compile the regular expressions, if needed
2066    for key in reVarStep:
2067        m = key.match(name)
2068        if m:
2069            return reVarStep[key]
2070    if parmDict is None: return None
2071    val = parmDict.get(key,0.0)
2072    if abs(val) > 0.05:
2073        return abs(val)/1000.
2074    else:
2075        return 1e-5
2076
2077def GenWildCard(varlist):
2078    '''Generate wildcard versions of G2 variables. These introduce '*'
2079    for a phase, histogram or atom number (but only for one of these
2080    fields) but only when there is more than one matching variable in the
2081    input variable list. So if the input is this::
2082
2083      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
2084
2085    then the output will be this::
2086
2087       wildList = ['*::AUiso:0', '0::AUiso:*']
2088
2089    :param list varlist: an input list of GSAS-II variable names
2090      (such as 0::AUiso:0)
2091
2092    :returns: wildList, the generated list of wild card variable names.
2093    '''
2094    wild = []
2095    for i in (0,1,3):
2096        currentL = varlist[:]
2097        while currentL:
2098            item1 = currentL.pop(0)
2099            i1splt = item1.split(':')
2100            if i >= len(i1splt): continue
2101            if i1splt[i]:
2102                nextL = []
2103                i1splt[i] = '[0-9]+'
2104                rexp = re.compile(':'.join(i1splt))
2105                matchlist = [item1]
2106                for nxtitem in currentL:
2107                    if rexp.match(nxtitem):
2108                        matchlist += [nxtitem]
2109                    else:
2110                        nextL.append(nxtitem)
2111                if len(matchlist) > 1:
2112                    i1splt[i] = '*'
2113                    wild.append(':'.join(i1splt))
2114                currentL = nextL
2115    return wild
2116
2117def LookupWildCard(varname,varlist):
2118    '''returns a list of variable names from list varname
2119    that match wildcard name in varname
2120
2121    :param str varname: a G2 variable name containing a wildcard
2122      (such as \\*::var)
2123    :param list varlist: the list of all variable names used in
2124      the current project
2125    :returns: a list of matching GSAS-II variables (may be empty)
2126    '''
2127    rexp = re.compile(varname.replace('*','[0-9]+'))
2128    return sorted([var for var in varlist if rexp.match(var)])
2129
2130def prmLookup(name,prmDict):
2131    '''Looks for a parameter in a min/max dictionary, optionally
2132    considering a wild card for histogram or atom number (use of
2133    both will never occur at the same time).
2134
2135    :param name: a GSAS-II parameter name (str, see :func:`getVarDescr`
2136      and :func:`CompileVarDesc`) or a :class:`G2VarObj` object.
2137    :param dict prmDict: a min/max dictionary, (parmMinDict
2138      or parmMaxDict in Controls) where keys are :class:`G2VarObj`
2139      objects.
2140    :returns: Two values, (**matchname**, **value**), are returned where:
2141
2142       * **matchname** *(str)* is the :class:`G2VarObj` object
2143         corresponding to the actual matched name,
2144         which could contain a wildcard even if **name** does not; and
2145       * **value** *(float)* which contains the parameter limit.
2146    '''
2147    for key,value in prmDict.items():
2148        if str(key) == str(name): return key,value
2149        if key == name: return key,value
2150    return None,None
2151       
2152
2153def _lookup(dic,key):
2154    '''Lookup a key in a dictionary, where None returns an empty string
2155    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
2156    '''
2157    if key is None:
2158        return ""
2159    elif key == "*":
2160        return "*"
2161    else:
2162        return dic.get(key,'?')
2163
2164def SortVariables(varlist):
2165    '''Sorts variable names in a sensible manner
2166    '''
2167    def cvnnums(var):
2168        v = []
2169        for i in var.split(':'):
2170            if i == '':
2171                v.append(-1)
2172                continue
2173            try:
2174                v.append(int(i))
2175            except:
2176                v.append(i)
2177        return v
2178    return sorted(varlist,key=cvnnums)
2179
2180class G2VarObj(object):
2181    '''Defines a GSAS-II variable either using the phase/atom/histogram
2182    unique Id numbers or using a character string that specifies
2183    variables by phase/atom/histogram number (which can change).
2184    Note that :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`,
2185    which calls :func:`IndexAllIds` (or
2186    :func:`GSASIIscriptable.G2Project.index_ids`) should be used to
2187    (re)load the current Ids
2188    before creating or later using the G2VarObj object.
2189
2190    This can store rigid body variables, but does not translate the residue # and
2191    body # to/from random Ids
2192
2193    A :class:`G2VarObj` object can be created with a single parameter:
2194
2195    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
2196      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
2197
2198     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
2199     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
2200     * a is the atom number (which may be left blank in which case the third colon is omitted).
2201       The atom number can be specified as '*' if a phase number is specified (not as '*').
2202       For rigid body variables, specify a will be a string of form "residue:body#"
2203
2204      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
2205      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
2206      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
2207      For a rigid body variables, AtomID is a string of form "residue:body#".
2208
2209    If four positional arguments are supplied, they are:
2210
2211    :param str/int phasenum: The number for the phase (or None or '*')
2212    :param str/int histnum: The number for the histogram (or None or '*')
2213    :param str varname: a single value can be used to create a :class:`G2VarObj`
2214    :param str/int atomnum: The number for the atom (or None or '*')
2215
2216    '''
2217    IDdict = {}
2218    IDdict['phases'] = {}
2219    IDdict['hists'] = {}
2220    IDdict['atoms'] = {}
2221    def __init__(self,*args):
2222        self.phase = None
2223        self.histogram = None
2224        self.name = ''
2225        self.atom = None
2226        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
2227            # single arg with 4 values
2228            self.phase,self.histogram,self.name,self.atom = args[0]
2229        elif len(args) == 1 and ':' in args[0]:
2230            #parse a string
2231            lst = args[0].split(':')
2232            if lst[0] == '*':
2233                self.phase = '*'
2234                if len(lst) > 3:
2235                    self.atom = lst[3]
2236                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2237            elif lst[1] == '*':
2238                self.histogram = '*'
2239                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2240            else:
2241                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2242                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2243                if len(lst) == 4:
2244                    if lst[3] == '*':
2245                        self.atom = '*'
2246                    else:
2247                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
2248                elif len(lst) == 5:
2249                    self.atom = lst[3]+":"+lst[4]
2250                elif len(lst) == 3:
2251                    pass
2252                else:
2253                    raise Exception("Incorrect number of colons in var name "+str(args[0]))
2254            self.name = lst[2]
2255        elif len(args) == 4:
2256            if args[0] == '*':
2257                self.phase = '*'
2258                self.atom = args[3]
2259            else:
2260                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
2261                if args[3] == '*':
2262                    self.atom = '*'
2263                elif args[0] is not None:
2264                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
2265            if args[1] == '*':
2266                self.histogram = '*'
2267            else:
2268                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
2269            self.name = args[2]
2270        else:
2271            raise Exception("Incorrectly called GSAS-II parameter name")
2272
2273        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
2274
2275    def __str__(self):
2276        return self.varname()
2277
2278    def __hash__(self):
2279        'Allow G2VarObj to be a dict key by implementing hashing'
2280        return hash(self.varname())
2281
2282    def varname(self):
2283        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
2284        string (p:h:<var>:a) or (p:h:<var>)
2285
2286        :returns: the variable name as a str
2287        '''
2288        a = ""
2289        if self.phase == "*":
2290            ph = "*"
2291            if self.atom:
2292                a = ":" + str(self.atom)
2293        else:
2294            ph = _lookup(PhaseRanIdLookup,self.phase)
2295            if self.atom == '*':
2296                a = ':*'
2297            elif self.atom:
2298                if ":" in str(self.atom):
2299                    a = ":" + str(self.atom)
2300                elif ph in AtomRanIdLookup:
2301                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
2302                else:
2303                    a = ":?"
2304        if self.histogram == "*":
2305            hist = "*"
2306        else:
2307            hist = _lookup(HistRanIdLookup,self.histogram)
2308        s = (ph + ":" + hist + ":" + str(self.name)) + a
2309        return s
2310
2311    def __repr__(self):
2312        '''Return the detailed contents of the object
2313        '''
2314        s = "<"
2315        if self.phase == '*':
2316            s += "Phases: all; "
2317            if self.atom is not None:
2318                if ":" in str(self.atom):
2319                    s += "Rigid body" + str(self.atom) + "; "
2320                else:
2321                    s += "Atom #" + str(self.atom) + "; "
2322        elif self.phase is not None:
2323            ph =  _lookup(PhaseRanIdLookup,self.phase)
2324            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
2325            if self.atom == '*':
2326                s += "Atoms: all; "
2327            elif ":" in str(self.atom):
2328                s += "Rigid body" + str(self.atom) + "; "
2329            elif self.atom is not None:
2330                s += "Atom rId=" + str(self.atom)
2331                if ph in AtomRanIdLookup:
2332                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
2333                else:
2334                    s += " (#? -- not found!); "
2335        if self.histogram == '*':
2336            s += "Histograms: all; "
2337        elif self.histogram is not None:
2338            hist = _lookup(HistRanIdLookup,self.histogram)
2339            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
2340        s += 'Variable name="' + str(self.name) + '">'
2341        return s+" ("+self.varname()+")"
2342
2343    def __eq__(self, other):
2344        '''Allow comparison of G2VarObj to other G2VarObj objects or strings.
2345        If any field is a wildcard ('*') that field matches.
2346        '''
2347        if type(other) is str:
2348            other = G2VarObj(other)
2349        elif type(other) is not G2VarObj:
2350            raise Exception("Invalid type ({}) for G2VarObj comparison with {}"
2351                            .format(type(other),other))
2352        if self.phase != other.phase and self.phase != '*' and other.phase != '*':
2353            return False
2354        if self.histogram != other.histogram and self.histogram != '*' and other.histogram != '*':
2355            return False
2356        if self.atom != other.atom and self.atom != '*' and other.atom != '*':
2357            return False
2358        if self.name != other.name:
2359            return False
2360        return True
2361
2362    def _show(self):
2363        'For testing, shows the current lookup table'
2364        print ('phases'+ self.IDdict['phases'])
2365        print ('hists'+ self.IDdict['hists'])
2366        print ('atomDict'+ self.IDdict['atoms'])
2367
2368#==========================================================================
2369def SetDefaultSample():
2370    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
2371    return {
2372        'InstrName':'',
2373        'ranId':ran.randint(0,sys.maxsize),
2374        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
2375        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],
2376        'Temperature':300.,'Pressure':0.1,'Time':0.0,
2377        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
2378        'Gonio. radius':200.0,
2379        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
2380#SASD items
2381        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
2382        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
2383        'Trans':1.0,                            #measured transmission
2384        'SlitLen':0.0,                          #Slit length - in Q(A-1)
2385        }
2386######################################################################
2387class ImportBaseclass(object):
2388    '''Defines a base class for the reading of input files (diffraction
2389    data, coordinates,...). See :ref:`Writing a Import Routine<import_routines>`
2390    for an explanation on how to use a subclass of this class.
2391    '''
2392    class ImportException(Exception):
2393        '''Defines an Exception that is used when an import routine hits an expected error,
2394        usually in .Reader.
2395
2396        Good practice is that the Reader should define a value in self.errors that
2397        tells the user some information about what is wrong with their file.
2398        '''
2399        pass
2400
2401    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
2402    def __init__(self,formatName,longFormatName=None,
2403                 extensionlist=[],strictExtension=False,):
2404        self.formatName = formatName # short string naming file type
2405        if longFormatName: # longer string naming file type
2406            self.longFormatName = longFormatName
2407        else:
2408            self.longFormatName = formatName
2409        # define extensions that are allowed for the file type
2410        # for windows, remove any extensions that are duplicate, as case is ignored
2411        if sys.platform == 'windows' and extensionlist:
2412            extensionlist = list(set([s.lower() for s in extensionlist]))
2413        self.extensionlist = extensionlist
2414        # If strictExtension is True, the file will not be read, unless
2415        # the extension matches one in the extensionlist
2416        self.strictExtension = strictExtension
2417        self.errors = ''
2418        self.warnings = ''
2419        self.SciPy = False          #image reader needed scipy
2420        # used for readers that will use multiple passes to read
2421        # more than one data block
2422        self.repeat = False
2423        self.selections = []
2424        self.repeatcount = 0
2425        self.readfilename = '?'
2426        self.scriptable = False
2427        #print 'created',self.__class__
2428
2429    def ReInitialize(self):
2430        'Reinitialize the Reader to initial settings'
2431        self.errors = ''
2432        self.warnings = ''
2433        self.SciPy = False          #image reader needed scipy
2434        self.repeat = False
2435        self.repeatcount = 0
2436        self.readfilename = '?'
2437
2438
2439#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
2440#        '''This method must be supplied in the child class to read the file.
2441#        if the read fails either return False or raise an Exception
2442#        preferably of type ImportException.
2443#        '''
2444#        #start reading
2445#        raise ImportException("Error occurred while...")
2446#        self.errors += "Hint for user on why the error occur
2447#        return False # if an error occurs
2448#        return True # if read OK
2449
2450    def ExtensionValidator(self, filename):
2451        '''This methods checks if the file has the correct extension
2452       
2453        :returns:
2454       
2455          * False if this filename will not be supported by this reader (only
2456            when strictExtension is True)
2457          * True if the extension matches the list supplied by the reader
2458          * None if the reader allows un-registered extensions
2459         
2460        '''
2461        if filename:
2462            ext = ospath.splitext(filename)[1]
2463            if not ext and self.strictExtension: return False
2464            for ext in self.extensionlist:               
2465                if sys.platform == 'windows':
2466                    if filename.lower().endswith(ext): return True
2467                else:
2468                    if filename.endswith(ext): return True
2469        if self.strictExtension:
2470            return False
2471        else:
2472            return None
2473
2474    def ContentsValidator(self, filename):
2475        '''This routine will attempt to determine if the file can be read
2476        with the current format.
2477        This will typically be overridden with a method that
2478        takes a quick scan of [some of]
2479        the file contents to do a "sanity" check if the file
2480        appears to match the selected format.
2481        the file must be opened here with the correct format (binary/text)
2482        '''
2483        #filepointer.seek(0) # rewind the file pointer
2484        return True
2485
2486    def CIFValidator(self, filepointer):
2487        '''A :meth:`ContentsValidator` for use to validate CIF files.
2488        '''
2489        filepointer.seek(0)
2490        for i,l in enumerate(filepointer):
2491            if i >= 1000: return True
2492            '''Encountered only blank lines or comments in first 1000
2493            lines. This is unlikely, but assume it is CIF anyway, since we are
2494            even less likely to find a file with nothing but hashes and
2495            blank lines'''
2496            line = l.strip()
2497            if len(line) == 0: # ignore blank lines
2498                continue
2499            elif line.startswith('#'): # ignore comments
2500                continue
2501            elif line.startswith('data_'): # on the right track, accept this file
2502                return True
2503            else: # found something invalid
2504                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
2505                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
2506                    self.errors += '  '+str(l)
2507                else:
2508                    self.errors += '  (binary)'
2509                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
2510                self.errors += '\n        a data_ statement begins a block.'
2511                return False
2512
2513######################################################################
2514class ImportPhase(ImportBaseclass):
2515    '''Defines a base class for the reading of files with coordinates
2516
2517    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
2518    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` and in
2519    :func:`GSASIIscriptable.import_generic`.
2520    See :ref:`Writing a Import Routine<import_routines>`
2521    for an explanation on how to use this class.
2522
2523    '''
2524    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2525        strictExtension=False,):
2526        # call parent __init__
2527        ImportBaseclass.__init__(self,formatName,longFormatName,
2528            extensionlist,strictExtension)
2529        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
2530        self.SymOps = {} # specified when symmetry ops are in file (e.g. CIF)
2531        self.Constraints = None
2532
2533######################################################################
2534class ImportStructFactor(ImportBaseclass):
2535    '''Defines a base class for the reading of files with tables
2536    of structure factors.
2537
2538    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
2539    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
2540    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2541    :meth:`Reader`.
2542
2543    See :ref:`Writing a Import Routine<import_routines>`
2544    for an explanation on how to use import classes in general. The specifics
2545    for reading a structure factor histogram require that
2546    the ``Reader()`` routine in the import
2547    class need to do only a few things: It
2548    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2549    and set :attr:`Parameters` with the instrument parameters
2550    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2551    '''
2552    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2553        strictExtension=False,):
2554        ImportBaseclass.__init__(self,formatName,longFormatName,
2555            extensionlist,strictExtension)
2556
2557        # define contents of Structure Factor entry
2558        self.Parameters = []
2559        'self.Parameters is a list with two dicts for data parameter settings'
2560        self.InitParameters()
2561        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2562        self.Banks = []             #for multi bank data (usually TOF)
2563        '''self.RefDict is a dict containing the reflection information, as read from the file.
2564        Item 'RefList' contains the reflection information. See the
2565        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
2566        for the contents of each row. Dict element 'FF'
2567        contains the form factor values for each element type; if this entry
2568        is left as initialized (an empty list) it will be initialized as needed later.
2569        '''
2570    def ReInitialize(self):
2571        'Reinitialize the Reader to initial settings'
2572        ImportBaseclass.ReInitialize(self)
2573        self.InitParameters()
2574        self.Banks = []             #for multi bank data (usually TOF)
2575        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2576
2577    def InitParameters(self):
2578        'initialize the instrument parameters structure'
2579        Lambda = 0.70926
2580        HistType = 'SXC'
2581        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2582                            'Lam':[Lambda,Lambda]
2583                            }, {}]
2584        'Parameters is a list with two dicts for data parameter settings'
2585
2586    def UpdateParameters(self,Type=None,Wave=None):
2587        'Revise the instrument parameters'
2588        if Type is not None:
2589            self.Parameters[0]['Type'] = [Type,Type]
2590        if Wave is not None:
2591            self.Parameters[0]['Lam'] = [Wave,Wave]
2592
2593######################################################################
2594class ImportPowderData(ImportBaseclass):
2595    '''Defines a base class for the reading of files with powder data.
2596
2597    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2598    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder` and in
2599    :func:`GSASIIscriptable.import_generic`.
2600    See :ref:`Writing a Import Routine<import_routines>`
2601    for an explanation on how to use this class.
2602    '''
2603    def __init__(self,formatName,longFormatName=None,
2604        extensionlist=[],strictExtension=False,):
2605        ImportBaseclass.__init__(self,formatName,longFormatName,
2606            extensionlist,strictExtension)
2607        self.clockWd = None  # used in TOF
2608        self.ReInitialize()
2609
2610    def ReInitialize(self):
2611        'Reinitialize the Reader to initial settings'
2612        ImportBaseclass.ReInitialize(self)
2613        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2614        self.powderdata = [] # Powder dataset
2615        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2616                np.array(x), # x-axis values
2617                np.array(y), # powder pattern intensities
2618                np.array(w), # 1/sig(intensity)^2 values (weights)
2619                np.array(yc), # calc. intensities (zero)
2620                np.array(yb), # calc. background (zero)
2621                np.array(yd), # obs-calc profiles
2622        '''
2623        self.comments = []
2624        self.idstring = ''
2625        self.Sample = SetDefaultSample() # default sample parameters
2626        self.Controls = {}  # items to be placed in top-level Controls
2627        self.GSAS = None     # used in TOF
2628        self.repeat_instparm = True # Should a parm file be
2629        #                             used for multiple histograms?
2630        self.instparm = None # name hint from file of instparm to use
2631        self.instfile = '' # full path name to instrument parameter file
2632        self.instbank = '' # inst parm bank number
2633        self.instmsg = ''  # a label that gets printed to show
2634                           # where instrument parameters are from
2635        self.numbanks = 1
2636        self.instdict = {} # place items here that will be transferred to the instrument parameters
2637        self.pwdparms = {} # place parameters that are transferred directly to the tree
2638                           # here (typically from an existing GPX file)
2639######################################################################
2640class ImportSmallAngleData(ImportBaseclass):
2641    '''Defines a base class for the reading of files with small angle data.
2642    See :ref:`Writing a Import Routine<import_routines>`
2643    for an explanation on how to use this class.
2644    '''
2645    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2646        strictExtension=False,):
2647
2648        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2649            strictExtension)
2650        self.ReInitialize()
2651
2652    def ReInitialize(self):
2653        'Reinitialize the Reader to initial settings'
2654        ImportBaseclass.ReInitialize(self)
2655        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2656        self.smallangledata = [] # SASD dataset
2657        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2658                np.array(x), # x-axis values
2659                np.array(y), # powder pattern intensities
2660                np.array(w), # 1/sig(intensity)^2 values (weights)
2661                np.array(yc), # calc. intensities (zero)
2662                np.array(yd), # obs-calc profiles
2663                np.array(yb), # preset bkg
2664        '''
2665        self.comments = []
2666        self.idstring = ''
2667        self.Sample = SetDefaultSample()
2668        self.GSAS = None     # used in TOF
2669        self.clockWd = None  # used in TOF
2670        self.numbanks = 1
2671        self.instdict = {} # place items here that will be transferred to the instrument parameters
2672
2673######################################################################
2674class ImportReflectometryData(ImportBaseclass):
2675    '''Defines a base class for the reading of files with reflectometry data.
2676    See :ref:`Writing a Import Routine<import_routines>`
2677    for an explanation on how to use this class.
2678    '''
2679    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2680        strictExtension=False,):
2681
2682        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2683            strictExtension)
2684        self.ReInitialize()
2685
2686    def ReInitialize(self):
2687        'Reinitialize the Reader to initial settings'
2688        ImportBaseclass.ReInitialize(self)
2689        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2690        self.reflectometrydata = [] # SASD dataset
2691        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2692                np.array(x), # x-axis values
2693                np.array(y), # powder pattern intensities
2694                np.array(w), # 1/sig(intensity)^2 values (weights)
2695                np.array(yc), # calc. intensities (zero)
2696                np.array(yd), # obs-calc profiles
2697                np.array(yb), # preset bkg
2698        '''
2699        self.comments = []
2700        self.idstring = ''
2701        self.Sample = SetDefaultSample()
2702        self.GSAS = None     # used in TOF
2703        self.clockWd = None  # used in TOF
2704        self.numbanks = 1
2705        self.instdict = {} # place items here that will be transferred to the instrument parameters
2706
2707######################################################################
2708class ImportPDFData(ImportBaseclass):
2709    '''Defines a base class for the reading of files with PDF G(R) data.
2710    See :ref:`Writing a Import Routine<import_routines>`
2711    for an explanation on how to use this class.
2712    '''
2713    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2714        strictExtension=False,):
2715
2716        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2717            strictExtension)
2718        self.ReInitialize()
2719
2720    def ReInitialize(self):
2721        'Reinitialize the Reader to initial settings'
2722        ImportBaseclass.ReInitialize(self)
2723        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2724        self.pdfdata = [] # PDF G(R) dataset
2725        '''A pdf g(r) data set is a list with items [x,y]:
2726                np.array(x), # r-axis values
2727                np.array(y), # pdf g(r)
2728        '''
2729        self.comments = []
2730        self.idstring = ''
2731        self.numbanks = 1
2732
2733######################################################################
2734class ImportImage(ImportBaseclass):
2735    '''Defines a base class for the reading of images
2736
2737    Images are read in only these places:
2738
2739      * Initial reading is typically done from a menu item
2740        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2741        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2742        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2743        :meth:`Reader`. This returns a list of reader objects for each read image.
2744        Also used in :func:`GSASIIscriptable.import_generic`.
2745
2746      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2747        directly into the data tree.
2748
2749      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2750
2751    When reading an image, the ``Reader()`` routine in the ImportImage class
2752    should set:
2753
2754      * :attr:`Comments`: a list of strings (str),
2755      * :attr:`Npix`: the number of pixels in the image (int),
2756      * :attr:`Image`: the actual image as a numpy array (np.array)
2757      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2758        data items are needed:
2759
2760         * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2761         * 'wavelength': wavelength in :math:`\\AA`.
2762         * 'distance': distance of detector from sample in cm.
2763         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2764         * 'size': size of image (such as ``[2048,2048]``).
2765         * 'ImageTag': image number or other keyword used to retrieve image from
2766           a multi-image data file (defaults to ``1`` if not specified).
2767         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2768
2769    optional data items:
2770
2771      * :attr:`repeat`: set to True if there are additional images to
2772        read in the file, False otherwise
2773      * :attr:`repeatcount`: set to the number of the image.
2774
2775    Note that the above is initialized with :meth:`InitParameters`.
2776    (Also see :ref:`Writing a Import Routine<import_routines>`
2777    for an explanation on how to use import classes in general.)
2778    '''
2779    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2780        strictExtension=False,):
2781        ImportBaseclass.__init__(self,formatName,longFormatName,
2782            extensionlist,strictExtension)
2783        self.InitParameters()
2784
2785    def ReInitialize(self):
2786        'Reinitialize the Reader to initial settings -- not used at present'
2787        ImportBaseclass.ReInitialize(self)
2788        self.InitParameters()
2789
2790    def InitParameters(self):
2791        'initialize the instrument parameters structure'
2792        self.Comments = ['No comments']
2793        self.Data = {}
2794        self.Npix = 0
2795        self.Image = None
2796        self.repeat = False
2797        self.repeatcount = 1
2798        self.sumfile = ''
2799
2800    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2801        '''Optionally, call this after reading in an image to load it into the tree.
2802        This saves time by preventing a reread of the same information.
2803        '''
2804        if ParentFrame:
2805            ParentFrame.ImageZ = self.Image   # store the image for plotting
2806            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2807            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2808
2809#################################################################################################
2810# shortcut routines
2811exp = np.exp
2812sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2813cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2814tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2815sqrt = sq = lambda x: np.sqrt(x)
2816pi = lambda: np.pi
2817
2818def FindFunction(f):
2819    '''Find the object corresponding to function f
2820
2821    :param str f: a function name such as 'numpy.exp'
2822    :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2823      that defines the package location(s) and where pkgobj
2824      defines the object associated with the function.
2825      If the function is not found, pkgobj is None.
2826    '''
2827    df = f.split('.')
2828    pkgdict = {}
2829    # no listed module name, try in current namespace
2830    if len(df) == 1:
2831        try:
2832            fxnobj = eval(f)
2833            return pkgdict,fxnobj
2834        except (AttributeError, NameError):
2835            return None,None
2836
2837    # includes a package, see if package is already imported
2838    pkgnam = '.'.join(df[:-1])
2839    try:
2840        fxnobj = eval(f)
2841        pkgdict[pkgnam] = eval(pkgnam)
2842        return pkgdict,fxnobj
2843    except (AttributeError, NameError):
2844        pass
2845    # package not yet imported, so let's try
2846    if '.' not in sys.path: sys.path.append('.')
2847    pkgnam = '.'.join(df[:-1])
2848    #for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2849    #    if pkgname:
2850    #        pkgname += '.' + pkg
2851    #    else:
2852    #        pkgname = pkg
2853    try:
2854        exec('import '+pkgnam)
2855        pkgdict[pkgnam] = eval(pkgnam)
2856        fxnobj = eval(f)
2857    except Exception as msg:
2858        print('load of '+pkgnam+' failed with error='+str(msg))
2859        return {},None
2860    # can we access the function? I am not exactly sure what
2861    #    I intended this to test originally (BHT)
2862    try:
2863        fxnobj = eval(f,globals(),pkgdict)
2864        return pkgdict,fxnobj
2865    except Exception as msg:
2866        print('call to',f,' failed with error=',str(msg))
2867        return None,None # not found
2868               
2869class ExpressionObj(object):
2870    '''Defines an object with a user-defined expression, to be used for
2871    secondary fits or restraints. Object is created null, but is changed
2872    using :meth:`LoadExpression`. This contains only the minimum
2873    information that needs to be stored to save and load the expression
2874    and how it is mapped to GSAS-II variables.
2875    '''
2876    def __init__(self):
2877        self.expression = ''
2878        'The expression as a text string'
2879        self.assgnVars = {}
2880        '''A dict where keys are label names in the expression mapping to a GSAS-II
2881        variable. The value a G2 variable name.
2882        Note that the G2 variable name may contain a wild-card and correspond to
2883        multiple values.
2884        '''
2885        self.freeVars = {}
2886        '''A dict where keys are label names in the expression mapping to a free
2887        parameter. The value is a list with:
2888
2889         * a name assigned to the parameter
2890         * a value for to the parameter and
2891         * a flag to determine if the variable is refined.
2892        '''
2893        self.depVar = None
2894
2895        self.lastError = ('','')
2896        '''Shows last encountered error in processing expression
2897        (list of 1-3 str values)'''
2898
2899        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2900        self.distance_atoms = None  # to be used for defining atom distances
2901
2902    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2903        '''Load the expression and associated settings into the object. Raises
2904        an exception if the expression is not parsed, if not all functions
2905        are defined or if not all needed parameter labels in the expression
2906        are defined.
2907
2908        This will not test if the variable referenced in these definitions
2909        are actually in the parameter dictionary. This is checked when the
2910        computation for the expression is done in :meth:`SetupCalc`.
2911
2912        :param str expr: the expression
2913        :param list exprVarLst: parameter labels found in the expression
2914        :param dict varSelect: this will be 0 for Free parameters
2915          and non-zero for expression labels linked to G2 variables.
2916        :param dict varName: Defines a name (str) associated with each free parameter
2917        :param dict varValue: Defines a value (float) associated with each free parameter
2918        :param dict varRefflag: Defines a refinement flag (bool)
2919          associated with each free parameter
2920        '''
2921        self.expression = expr
2922        self.compiledExpr = None
2923        self.freeVars = {}
2924        self.assgnVars = {}
2925        for v in exprVarLst:
2926            if varSelect[v] == 0:
2927                self.freeVars[v] = [
2928                    varName.get(v),
2929                    varValue.get(v),
2930                    varRefflag.get(v),
2931                    ]
2932            else:
2933                self.assgnVars[v] = varName[v]
2934        self.CheckVars()
2935
2936    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2937        '''Load the expression and associated settings from the object into
2938        arrays used for editing.
2939
2940        :param list exprVarLst: parameter labels found in the expression
2941        :param dict varSelect: this will be 0 for Free parameters
2942          and non-zero for expression labels linked to G2 variables.
2943        :param dict varName: Defines a name (str) associated with each free parameter
2944        :param dict varValue: Defines a value (float) associated with each free parameter
2945        :param dict varRefflag: Defines a refinement flag (bool)
2946          associated with each free parameter
2947
2948        :returns: the expression as a str
2949        '''
2950        for v in self.freeVars:
2951            varSelect[v] = 0
2952            varName[v] = self.freeVars[v][0]
2953            varValue[v] = self.freeVars[v][1]
2954            varRefflag[v] = self.freeVars[v][2]
2955        for v in self.assgnVars:
2956            varSelect[v] = 1
2957            varName[v] = self.assgnVars[v]
2958        return self.expression
2959
2960    def GetVaried(self):
2961        'Returns the names of the free parameters that will be refined'
2962        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
2963
2964    def GetVariedVarVal(self):
2965        'Returns the names and values of the free parameters that will be refined'
2966        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
2967
2968    def UpdateVariedVars(self,varyList,values):
2969        'Updates values for the free parameters (after a refinement); only updates refined vars'
2970        for v in self.freeVars:
2971            if not self.freeVars[v][2]: continue
2972            if "::"+self.freeVars[v][0] not in varyList: continue
2973            indx = list(varyList).index("::"+self.freeVars[v][0])
2974            self.freeVars[v][1] = values[indx]
2975
2976    def GetIndependentVars(self):
2977        'Returns the names of the required independent parameters used in expression'
2978        return [self.assgnVars[v] for v in self.assgnVars]
2979
2980    def CheckVars(self):
2981        '''Check that the expression can be parsed, all functions are
2982        defined and that input loaded into the object is internally
2983        consistent. If not an Exception is raised.
2984
2985        :returns: a dict with references to packages needed to
2986          find functions referenced in the expression.
2987        '''
2988        ret = self.ParseExpression(self.expression)
2989        if not ret:
2990            raise Exception("Expression parse error")
2991        exprLblList,fxnpkgdict = ret
2992        # check each var used in expression is defined
2993        defined = list(self.assgnVars.keys()) + list(self.freeVars.keys())
2994        notfound = []
2995        for var in exprLblList:
2996            if var not in defined:
2997                notfound.append(var)
2998        if notfound:
2999            msg = 'Not all variables defined'
3000            msg1 = 'The following variables were not defined: '
3001            msg2 = ''
3002            for var in notfound:
3003                if msg: msg += ', '
3004                msg += var
3005            self.lastError = (msg1,'  '+msg2)
3006            raise Exception(msg)
3007        return fxnpkgdict
3008
3009    def ParseExpression(self,expr):
3010        '''Parse an expression and return a dict of called functions and
3011        the variables used in the expression. Returns None in case an error
3012        is encountered. If packages are referenced in functions, they are loaded
3013        and the functions are looked up into the modules global
3014        workspace.
3015
3016        Note that no changes are made to the object other than
3017        saving an error message, so that this can be used for testing prior
3018        to the save.
3019
3020        :returns: a list of used variables
3021        '''
3022        self.lastError = ('','')
3023        import ast
3024        def ASTtransverse(node,fxn=False):
3025            '''Transverse a AST-parsed expresson, compiling a list of variables
3026            referenced in the expression. This routine is used recursively.
3027
3028            :returns: varlist,fxnlist where
3029              varlist is a list of referenced variable names and
3030              fxnlist is a list of used functions
3031            '''
3032            varlist = []
3033            fxnlist = []
3034            if isinstance(node, list):
3035                for b in node:
3036                    v,f = ASTtransverse(b,fxn)
3037                    varlist += v
3038                    fxnlist += f
3039            elif isinstance(node, ast.AST):
3040                for a, b in ast.iter_fields(node):
3041                    if isinstance(b, ast.AST):
3042                        if a == 'func':
3043                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
3044                            continue
3045                        v,f = ASTtransverse(b,fxn)
3046                        varlist += v
3047                        fxnlist += f
3048                    elif isinstance(b, list):
3049                        v,f = ASTtransverse(b,fxn)
3050                        varlist += v
3051                        fxnlist += f
3052                    elif node.__class__.__name__ == "Name":
3053                        varlist += [b]
3054                    elif fxn and node.__class__.__name__ == "Attribute":
3055                        varlist += [b]
3056            return varlist,fxnlist
3057        try:
3058            exprast = ast.parse(expr)
3059        except SyntaxError:
3060            s = ''
3061            import traceback
3062            for i in traceback.format_exc().splitlines()[-3:-1]:
3063                if s: s += "\n"
3064                s += str(i)
3065            self.lastError = ("Error parsing expression:",s)
3066            return
3067        # find the variables & functions
3068        v,f = ASTtransverse(exprast)
3069        varlist = sorted(list(set(v)))
3070        fxnlist = list(set(f))
3071        pkgdict = {}
3072        # check the functions are defined
3073        for fxn in fxnlist:
3074            fxndict,fxnobj = FindFunction(fxn)
3075            if not fxnobj:
3076                self.lastError = ("Error: Invalid function",fxn,
3077                                  "is not defined")
3078                return
3079            if not hasattr(fxnobj,'__call__'):
3080                self.lastError = ("Error: Not a function.",fxn,
3081                                  "cannot be called as a function")
3082                return
3083            pkgdict.update(fxndict)
3084        return varlist,pkgdict
3085
3086    def GetDepVar(self):
3087        'return the dependent variable, or None'
3088        return self.depVar
3089
3090    def SetDepVar(self,var):
3091        'Set the dependent variable, if used'
3092        self.depVar = var
3093#==========================================================================
3094class ExpressionCalcObj(object):
3095    '''An object used to evaluate an expression from a :class:`ExpressionObj`
3096    object.
3097
3098    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
3099      an expression string and mappings for the parameter labels in that object.
3100    '''
3101    def __init__(self,exprObj):
3102        self.eObj = exprObj
3103        'The expression and mappings; a :class:`ExpressionObj` object'
3104        self.compiledExpr = None
3105        'The expression as compiled byte-code'
3106        self.exprDict = {}
3107        '''dict that defines values for labels used in expression and packages
3108        referenced by functions
3109        '''
3110        self.lblLookup = {}
3111        '''Lookup table that specifies the expression label name that is
3112        tied to a particular GSAS-II parameters in the parmDict.
3113        '''
3114        self.fxnpkgdict = {}
3115        '''a dict with references to packages needed to
3116        find functions referenced in the expression.
3117        '''
3118        self.varLookup = {}
3119        '''Lookup table that specifies the GSAS-II variable(s)
3120        indexed by the expression label name. (Used for only for diagnostics
3121        not evaluation of expression.)
3122        '''
3123        self.su = None
3124        '''Standard error evaluation where supplied by the evaluator
3125        '''
3126        # Patch: for old-style expressions with a (now removed step size)
3127        if '2' in platform.python_version_tuple()[0]: 
3128            basestr = basestring
3129        else:
3130            basestr = str
3131        for v in self.eObj.assgnVars:
3132            if not isinstance(self.eObj.assgnVars[v], basestr):
3133                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
3134        self.parmDict = {}
3135        '''A copy of the parameter dictionary, for distance and angle computation
3136        '''
3137
3138    def SetupCalc(self,parmDict):
3139        '''Do all preparations to use the expression for computation.
3140        Adds the free parameter values to the parameter dict (parmDict).
3141        '''
3142        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3143            return
3144        self.fxnpkgdict = self.eObj.CheckVars()
3145        # all is OK, compile the expression
3146        self.compiledExpr = compile(self.eObj.expression,'','eval')
3147
3148        # look at first value in parmDict to determine its type
3149        parmsInList = True
3150        if '2' in platform.python_version_tuple()[0]: 
3151            basestr = basestring
3152        else:
3153            basestr = str
3154        for key in parmDict:
3155            val = parmDict[key]
3156            if isinstance(val, basestr):
3157                parmsInList = False
3158                break
3159            try: # check if values are in lists
3160                val = parmDict[key][0]
3161            except (TypeError,IndexError):
3162                parmsInList = False
3163            break
3164
3165        # set up the dicts needed to speed computations
3166        self.exprDict = {}
3167        self.lblLookup = {}
3168        self.varLookup = {}
3169        for v in self.eObj.freeVars:
3170            varname = self.eObj.freeVars[v][0]
3171            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
3172            self.lblLookup[varname] = v
3173            self.varLookup[v] = varname
3174            if parmsInList:
3175                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
3176            else:
3177                parmDict[varname] = self.eObj.freeVars[v][1]
3178            self.exprDict[v] = self.eObj.freeVars[v][1]
3179        for v in self.eObj.assgnVars:
3180            varname = self.eObj.assgnVars[v]
3181            if varname in parmDict:
3182                self.lblLookup[varname] = v
3183                self.varLookup[v] = varname
3184                if parmsInList:
3185                    self.exprDict[v] = parmDict[varname][0]
3186                else:
3187                    self.exprDict[v] = parmDict[varname]
3188            elif '*' in varname:
3189                varlist = LookupWildCard(varname,list(parmDict.keys()))
3190                if len(varlist) == 0:
3191                    raise Exception("No variables match "+str(v))
3192                for var in varlist:
3193                    self.lblLookup[var] = v
3194                if parmsInList:
3195                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
3196                else:
3197                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
3198                self.varLookup[v] = [var for var in varlist]
3199            else:
3200                self.exprDict[v] = None
3201#                raise Exception,"No value for variable "+str(v)
3202        self.exprDict.update(self.fxnpkgdict)
3203
3204    def UpdateVars(self,varList,valList):
3205        '''Update the dict for the expression with a set of values
3206        :param list varList: a list of variable names
3207        :param list valList: a list of corresponding values
3208        '''
3209        for var,val in zip(varList,valList):
3210            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
3211
3212    def UpdateDict(self,parmDict):
3213        '''Update the dict for the expression with values in a dict
3214        :param dict parmDict: a dict of values, items not in use are ignored
3215        '''
3216        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3217            self.parmDict = parmDict
3218            return
3219        for var in parmDict:
3220            if var in self.lblLookup:
3221                self.exprDict[self.lblLookup[var]] = parmDict[var]
3222
3223    def EvalExpression(self):
3224        '''Evaluate an expression. Note that the expression
3225        and mapping are taken from the :class:`ExpressionObj` expression object
3226        and the parameter values were specified in :meth:`SetupCalc`.
3227        :returns: a single value for the expression. If parameter
3228        values are arrays (for example, from wild-carded variable names),
3229        the sum of the resulting expression is returned.
3230
3231        For example, if the expression is ``'A*B'``,
3232        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
3233
3234        [0.5, 1, 0.5]
3235
3236        then the result will be ``4.0``.
3237        '''
3238        self.su = None
3239        if self.eObj.expression.startswith('Dist'):
3240#            GSASIIpath.IPyBreak()
3241            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
3242            return dist
3243        elif self.eObj.expression.startswith('Angle'):
3244            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
3245            return angle
3246        if self.compiledExpr is None:
3247            raise Exception("EvalExpression called before SetupCalc")
3248        try:
3249            val = eval(self.compiledExpr,globals(),self.exprDict)
3250        except TypeError:
3251            val = None
3252        if not np.isscalar(val):
3253            val = np.sum(val)
3254        return val
3255
3256class G2Exception(Exception):
3257    'A generic GSAS-II exception class'
3258    def __init__(self,msg):
3259        self.msg = msg
3260    def __str__(self):
3261        return repr(self.msg)
3262
3263class G2RefineCancel(Exception):
3264    'Raised when Cancel is pressed in a refinement dialog'
3265    def __init__(self,msg):
3266        self.msg = msg
3267    def __str__(self):
3268        return repr(self.msg)
3269   
3270def HowDidIgetHere(wherecalledonly=False):
3271    '''Show a traceback with calls that brought us to the current location.
3272    Used for debugging.
3273    '''
3274    import traceback
3275    if wherecalledonly:
3276        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
3277        print(i.strip().rstrip())
3278    else:
3279        print (70*'*')
3280        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
3281        print (70*'*')
3282
3283# Note that this is GUI code and should be moved at somepoint
3284def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
3285    '''Create and initialize a new set of PDF tree entries
3286
3287    :param Frame G2frame: main GSAS-II tree frame object
3288    :param str PWDRtree: name of PWDR to be used to create PDF item
3289    :param dict ElList: data structure with composition
3290    :param list Qlimits: Q limits to be used for computing the PDF
3291    :param float numAtm: no. atom in chemical formula
3292    :param float FltBkg: flat background value
3293    :param list PDFnames: previously used PDF names
3294
3295    :returns: the Id of the newly created PDF entry
3296    '''
3297    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
3298    if PDFname in PDFnames:
3299        print('Skipping, entry already exists: '+PDFname)
3300        return None
3301    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
3302    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
3303    Data = {
3304        'Sample':{'Name':PWDRtree,'Mult':1.0},
3305        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
3306        'Container':{'Name':'','Mult':-1.0,'Refine':False},
3307        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
3308        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
3309        'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
3310        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,'Rmin':1.0,
3311        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
3312    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
3313    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
3314        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
3315    return Id
3316#%%
3317class ShowTiming(object):
3318    '''An object to use for timing repeated sections of code.
3319
3320    Create the object with::
3321       tim0 = ShowTiming()
3322
3323    Tag sections of code to be timed with::
3324       tim0.start('start')
3325       tim0.start('in section 1')
3326       tim0.start('in section 2')
3327       
3328    etc. (Note that each section should have a unique label.)
3329
3330    After the last section, end timing with::
3331       tim0.end()
3332
3333    Show timing results with::
3334       tim0.show()
3335       
3336    '''
3337    def __init__(self):
3338        self.timeSum =  []
3339        self.timeStart = []
3340        self.label = []
3341        self.prev = None
3342    def start(self,label):
3343        import time
3344        if label in self.label:
3345            i = self.label.index(label)
3346            self.timeStart[i] = time.time()
3347        else:
3348            i = len(self.label)
3349            self.timeSum.append(0.0)
3350            self.timeStart.append(time.time())
3351            self.label.append(label)
3352        if self.prev is not None:
3353            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
3354        self.prev = i
3355    def end(self):
3356        import time
3357        if self.prev is not None:
3358            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
3359        self.prev = None
3360    def show(self):
3361        sumT = sum(self.timeSum)
3362        print('Timing results (total={:.2f} sec)'.format(sumT))
3363        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
3364            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
3365#%%
3366
3367def validateAtomDrawType(typ,generalData={}):
3368    '''Confirm that the selected Atom drawing type is valid for the current
3369    phase. If not, use 'vdW balls'. This is currently used only for setting a
3370    default when atoms are added to the atoms draw list.
3371    '''
3372    if typ in ('lines','vdW balls','sticks','balls & sticks','ellipsoids'):
3373        return typ
3374    # elif generalData.get('Type','') == 'macromolecular':
3375    #     if typ in ('backbone',):
3376    #         return typ
3377    return 'vdW balls'
3378
3379if __name__ == "__main__":
3380    # test variable descriptions
3381    for var in '0::Afrac:*',':1:Scale','1::dAx:0','::undefined':
3382        v = var.split(':')[2]
3383        print(var+':\t', getDescr(v),getVarStep(v))
3384    import sys; sys.exit()
3385    # test equation evaluation
3386    def showEQ(calcobj):
3387        print (50*'=')
3388        print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
3389        for v in sorted(calcobj.varLookup):
3390            print ("  "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
3391        # print '  Derivatives'
3392        # for v in calcobj.derivStep.keys():
3393        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
3394
3395    obj = ExpressionObj()
3396
3397    obj.expression = "A*np.exp(B)"
3398    obj.assgnVars =  {'B': '0::Afrac:1'}
3399    obj.freeVars =  {'A': [u'A', 0.5, True]}
3400    #obj.CheckVars()
3401    calcobj = ExpressionCalcObj(obj)
3402
3403    obj1 = ExpressionObj()
3404    obj1.expression = "A*np.exp(B)"
3405    obj1.assgnVars =  {'B': '0::Afrac:*'}
3406    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
3407    #obj.CheckVars()
3408    calcobj1 = ExpressionCalcObj(obj1)
3409
3410    obj2 = ExpressionObj()
3411    obj2.distance_stuff = np.array([[0,1],[1,-1]])
3412    obj2.expression = "Dist(1,2)"
3413    GSASIIpath.InvokeDebugOpts()
3414    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3415    calcobj2 = ExpressionCalcObj(obj2)
3416    calcobj2.SetupCalc(parmDict2)
3417    showEQ(calcobj2)
3418
3419    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
3420    print ('\nDict = '+parmDict1)
3421    calcobj.SetupCalc(parmDict1)
3422    showEQ(calcobj)
3423    calcobj1.SetupCalc(parmDict1)
3424    showEQ(calcobj1)
3425
3426    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3427    print ('Dict = '+parmDict2)
3428    calcobj.SetupCalc(parmDict2)
3429    showEQ(calcobj)
3430    calcobj1.SetupCalc(parmDict2)
3431    showEQ(calcobj1)
3432    calcobj2.SetupCalc(parmDict2)
3433    showEQ(calcobj2)
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