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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2022-01-19 22:56:37 +0000 (Wed, 19 Jan 2022) $
5# $Author: toby $
6# $Revision: 5148 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 5148 2022-01-19 22:56:37Z toby $
9########### SVN repository information ###################
10
11'''
12*GSASIIobj: Data objects*
13=========================
14
15This module defines and/or documents the data structures used in GSAS-II, as well
16as provides misc. support routines.
17
18.. Next command allows \\AA to be used in HTML
19
20.. only:: html
21
22   :math:`\\require{mediawiki-texvc}`
23
24.. _Constraints_table:
25
26.. index::
27   single: Constraints object description
28   single: Data object descriptions; Constraints
29
30Constraints Tree Item
31----------------------
32
33Constraints are stored in a dict, separated into groups.
34Note that parameter are named in the following pattern,
35p:h:<var>:n, where p is the phase number, h is the histogram number
36<var> is a variable name and n is the parameter number.
37If a parameter does not depend on a histogram or phase or is unnumbered, that
38number is omitted.
39Note that the contents of each dict item is a List where each element in the
40list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
41The constraints in this form are converted in
42:func:`GSASIImapvars.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
43
44The keys in the Constraints dict are:
45
46.. tabularcolumns:: |l|p{4.5in}|
47
48==========  ====================================================
49  key         explanation
50==========  ====================================================
51Hist        This specifies a list of constraints on
52            histogram-related parameters,
53            which will be of form :h:<var>:n.
54HAP         This specifies a list of constraints on parameters
55            that are defined for every histogram in each phase
56            and are of form p:h:<var>:n.
57Phase       This specifies a list of constraints on phase
58            parameters,
59            which will be of form p::<var>:n.
60Global      This specifies a list of constraints on parameters
61            that are not tied to a histogram or phase and
62            are of form ::<var>:n
63==========  ====================================================
64
65.. _Constraint_definitions_table:
66
67.. index::
68   single: Constraint definition object description
69   single: Data object descriptions; Constraint Definition
70
71Each constraint is defined as an item in a list. Each constraint is of form::
72
73[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
74
75Where the variable pair list item containing two values [<mult>, <var>], where:
76
77  * <mult> is a multiplier for the constraint (float)
78  * <var> a :class:`G2VarObj` object. (Note that in very old .gpx files this might be a str with a variable name of form 'p:h:name[:at]')
79
80Note that the last three items in the list play a special role:
81
82 * <fixedval> is the fixed value for a `constant equation` (``constype=c``)
83   constraint or is None. For a `New variable` (``constype=f``) constraint,
84   a variable name can be specified as a str (used for externally
85   generated constraints)
86 * <varyflag> is True or False for `New variable` (``constype=f``) constraints
87   or is None. This indicates if this variable should be refined.
88 * <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
89
90    * 'e' defines a set of equivalent variables. Only the first variable is refined (if the
91      appropriate refine flag is set) and and all other equivalent variables in the list
92      are generated from that variable, using the appropriate multipliers.
93    * 'c' defines a constraint equation of form,
94      :math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
95    * 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
96      even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
97      constraint and the mult value is ignored.
98      This is of particular value when needing to hold one or more variables where a
99      single flag controls a set of variables such as, coordinates,
100      the reciprocal metric tensor or anisotropic displacement parameter.
101    * 'f' defines a new variable (function) according to relationship
102      :math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
103
104.. _Covariance_table:
105
106.. index::
107   single: Covariance description
108   single: Data object descriptions; Covariance
109
110Covariance Tree Item
111--------------------
112
113The Covariance tree item has results from the last least-squares run. They
114are stored in a dict with these keys:
115
116.. tabularcolumns:: |l|l|p{4in}|
117
118=============  ===============  ====================================================
119  key            sub-key        explanation
120=============  ===============  ====================================================
121newCellDict    \\                (dict) ith lattice parameters computed by
122                                :func:`GSASIIstrMath.GetNewCellParms`
123title          \\                (str) Name of gpx file(?)
124variables      \\                (list) Values for all N refined variables
125                                (list of float values, length N,
126                                ordered to match varyList)
127sig            \\                (list) Uncertainty values for all N refined variables
128                                (list of float values, length N,
129                                ordered to match varyList)
130varyList       \\                (list of str values, length N) List of directly refined variables
131                               
132newAtomDict    \\                (dict) atom position values computed in
133                                :func:`GSASIIstrMath.ApplyXYZshifts`
134Rvals          \\                (dict) R-factors, GOF, Marquardt value for last
135                                refinement cycle
136\\              Nobs             (int) Number of observed data points
137\\              Rwp              (float) overall weighted profile R-factor (%)
138\\              chisq            (float) :math:`\\sum w*(I_{obs}-I_{calc})^2`                               
139                                for all data.
140                                Note: this is not the reduced :math:`\\chi^2`.
141\\              lamMax           (float) Marquardt value applied to Hessian diagonal
142\\              GOF              (float) The goodness-of-fit, aka square root of
143                                the reduced chi squared.
144covMatrix      \\                (np.array) The (NxN) covVariance matrix
145=============  ===============  ====================================================
146
147.. _Phase_table:
148
149.. index::
150   single: Phase object description
151   single: Data object descriptions; Phase
152
153Phase Tree Items
154----------------
155
156Phase information is stored in the GSAS-II data tree as children of the
157Phases item in a dict with keys:
158
159.. tabularcolumns:: |l|l|p{4in}|
160
161==========  ===============     =====================================================================================================
162  key         sub-key           explanation
163==========  ===============     =====================================================================================================
164General         \\               (dict) Overall information for the phase
165  \\         3Dproj              (list of str) projections for 3D pole distribution plots
166  \\         AngleRadii          (list of floats) Default radius for each atom used to compute
167                                interatomic angles
168  \\         AtomMass            (list of floats) Masses for atoms
169  \\         AtomPtrs            (list of int) four locations (cx,ct,cs & cu) to use to pull info
170                                from the atom records
171  \\         AtomTypes           (llist of str) Atom types
172  \\         BondRadii           (list of floats) Default radius for each atom used to compute
173                                interatomic distances
174  \\         Cell                Unit cell parameters & ref. flag
175                                (list with 8 items. All but first item are float.)
176
177                                 0: cell refinement flag (True/False),
178                                 1-3: a, b, c, (:math:`\\AA`)
179                                 4-6: alpha, beta & gamma, (degrees)
180                                 7: volume (:math:`\\AA^3`)
181  \\         Color               (list of (r,b,g) triplets) Colors for atoms
182  \\         Compare             (dict) Polygon comparison parameters
183  \\         Data plot type      (str) data plot type ('Mustrain', 'Size' or
184                                'Preferred orientation') for powder data
185  \\         DisAglCtls          (dDict) with distance/angle search controls,
186                                which has keys 'Name', 'AtomTypes',
187                                'BondRadii', 'AngleRadii' which are as above
188                                except are possibly edited. Also contains
189                                'Factors', which is a 2 element list with
190                                a multiplier for bond and angle search range
191                                [typically (0.85,0.85)].
192  \\         F000X               (float) x-ray F(000) intensity
193  \\         F000N               (float) neutron F(000) intensity
194  \\         Flip                (dict) Charge flip controls
195  \\         HydIds              (dict) geometrically generated hydrogen atoms
196  \\         Isotope             (dict) Isotopes for each atom type
197  \\         Isotopes            (dict) Scattering lengths for each isotope
198                                combination for each element in phase
199  \\         MCSA controls       (dict) Monte Carlo-Simulated Annealing controls
200  \\         Map                 (dict) Map parameters
201  \\         Mass                (float) Mass of unit cell contents in g/mol
202  \\         Modulated           (bool) True if phase modulated
203  \\         Mydir               (str) Directory of current .gpx file
204  \\         Name                (str) Phase name
205  \\         NoAtoms             (dict) Number of atoms per unit cell of each type
206  \\         POhkl               (list) March-Dollase preferred orientation direction
207  \\         Pawley dmin         (float) maximum Q (as d-space) to use for Pawley extraction
208  \\         Pawley dmax         (float) minimum Q (as d-space) to use for Pawley extraction
209  \\         Pawley neg wt       (float) Restraint value for negative Pawley intensities
210  \\         SGData              (object) Space group details as a
211                                :ref:`space group (SGData) <SGData_table>`
212                                object, as defined in :func:`GSASIIspc.SpcGroup`.
213  \\         SH Texture          (dict) Spherical harmonic preferred orientation parameters
214  \\         Super               (int) dimension of super group (0,1 only)
215  \\         Type                (str) phase type (e.g. 'nuclear')
216  \\         Z                   (dict) Atomic numbers for each atom type
217  \\         doDysnomia          (bool) flag for max ent map modification via Dysnomia
218  \\         doPawley            (bool) Flag for Pawley intensity extraction
219  \\         vdWRadii            (dict) Van der Waals radii for each atom type
220ranId           \\               (int) unique random number Id for phase
221pId             \\               (int) Phase Id number for current project.
222Atoms           \\               (list of lists) Atoms in phase as a list of lists. The outer list
223                                is for each atom, the inner list contains varying
224                                items depending on the type of phase, see
225                                the :ref:`Atom Records <Atoms_table>` description.
226Drawing         \\               (dict) Display parameters
227\\           Atoms               (list of lists) with an entry for each atom that is drawn
228\\           Plane               (list) Controls for contour density plane display
229\\           Quaternion          (4 element np.array) Viewing quaternion
230\\           Zclip               (float) clipping distance in :math:`\\AA`
231\\           Zstep               (float) Step to de/increase Z-clip
232\\           atomPtrs            (list) positions of x, type, site sym, ADP flag in Draw Atoms
233\\           backColor           (list) background for plot as and R,G,B triplet
234                                (default = [0, 0, 0], black).
235\\           ballScale           (float) Radius of spheres in ball-and-stick display
236\\           bondList            (dict) Bonds
237\\           bondRadius          (float) Radius of binds in :math:`\\AA`
238\\           cameraPos           (float) Viewing position in :math:`\\AA` for plot
239\\           contourLevel        (float) map contour level in :math:`e/\\AA^3`
240\\           contourMax          (float) map contour maximum
241\\           depthFog            (bool) True if use depthFog on plot - set currently as False
242\\           ellipseProb         (float) Probability limit for display of thermal
243                                ellipsoids in % .
244\\           magMult             (float) multiplier for magnetic moment arrows
245\\           mapSize             (float) x & y dimensions of contourmap (fixed internally)
246\\           modelView           (4,4 array) from openGL drawing transofmation matrix
247\\           oldxy               (list with two floats) previous view point
248\\           radiusFactor        (float) Distance ratio for searching for bonds. Bonds
249                                are located that are within r(Ra+Rb) and (Ra+Rb)/r
250                                where Ra and Rb are the atomic radii.
251\\           selectedAtoms       (list of int values) List of selected atoms
252\\           showABC             (bool) Flag to show view point triplet. True=show.
253\\           showHydrogen        (bool) Flag to control plotting of H atoms.
254\\           showRigidBodies     (bool) Flag to highlight rigid body placement
255\\           showSlice           (bool) flag to show contour map
256\\           sizeH               (float) Size ratio for H atoms
257\\           unitCellBox         (bool) Flag to control display of the unit cell.
258\\           vdwScale            (float) Multiplier of van der Waals radius for display of vdW spheres.
259\\           viewDir             (np.array with three floats) cartesian viewing direction
260\\           viewPoint           (list of lists) First item in list is [x,y,z]
261                                 in fractional coordinates for the center of
262                                 the plot. Second item list of previous & current
263                                 atom number viewed (may be [0,0])
264ISODISTORT      \\               (dict) contains controls for running ISODISTORT and results from it
265\\           ISOmethod           (int) ISODISTORT method (currently 1 or 4; 2 & 3 not implemented in GSAS-II)
266\\           ParentCIF           (str) parent cif file name for ISODISTORT method 4
267\\           ChildCIF            (str) child cif file name for ISODISTORT method 4
268\\           SGselect            (dict) selection list for lattice types in radio result from ISODISTORT method 1
269\\           selection           (int) chosen selection from radio
270\\           radio               (list) results from ISODISTORT method 1
271\\           ChildMatrix         (3x3 array) transformation matrix for method 3 (not currently used)
272\\           ChildSprGp          (str) child space group for method 3 (not currently used)
273\\           ChildCell           (str) cell ordering for nonstandard orthorhombic ChildSprGrp in method 3 (not currently used)
274\\           G2ModeList          (list) ISODISTORT mode names
275\\           modeDispl           (list) distortion mode values; refinable parameters
276\\           ISOmodeDispl        (list) distortion mode values as determined in method 4 by ISODISTORT
277\\           NormList            (list) ISODISTORT normalization values; to convert mode value to fractional coordinate dsplacement
278\\           G2parentCoords      (list) full set of parent structure coordinates transformed to child structure; starting basis for mode displacements
279\\           G2VarList           (list)
280\\           IsoVarList          (list)
281\\           G2coordOffset       (list) only adjustible set of parent structure coordinates
282\\           G2OccVarList        (list)
283\\           Var2ModeMatrix      (array) atom variable to distortion mode transformation
284\\           Mode2VarMatrix      (array) distortion mode to atom variable transformation
285\\           rundata             (dict) saved input information for use by ISODISTORT method 1
286
287RBModels        \\               Rigid body assignments (note Rigid body definitions
288                                are stored in their own main top-level tree entry.)
289RMC             \\               (dict) RMCProfile, PDFfit & fullrmc controls
290Pawley ref      \\               (list) Pawley reflections
291Histograms      \\               (dict of dicts) The key for the outer dict is
292                                the histograms tied to this phase. The inner
293                                dict contains the combined phase/histogram
294                                parameters for items such as scale factors,
295                                size and strain parameters. The following are the
296                                keys to the inner dict. (dict)
297\\           Babinet             (dict) For protein crystallography. Dictionary with two
298                                entries, 'BabA', 'BabU'
299\\           Extinction          (list of float, bool) Extinction parameter
300\\           Flack               (list of [float, bool]) Flack parameter & refine flag
301\\           HStrain             (list of two lists) Hydrostatic strain. The first is
302                                a list of the HStrain parameters (1, 2, 3, 4, or 6
303                                depending on unit cell), the second is a list of boolean
304                                refinement parameters (same length)
305\\           Histogram           (str) The name of the associated histogram
306\\           Layer Disp          (list of [float, bool]) Layer displacement in beam direction & refine flag
307\\           LeBail              (bool) Flag for LeBail extraction
308\\           Mustrain            (list) Microstrain parameters, in order:
309   
310                                0. Type, one of  u'isotropic', u'uniaxial', u'generalized'
311                                1. Isotropic/uniaxial parameters - list of 3 floats
312                                2. Refinement flags - list of 3 bools
313                                3. Microstrain axis - list of 3 ints, [h, k, l]
314                                4. Generalized mustrain parameters - list of 2-6 floats, depending on space group
315                                5. Generalized refinement flags - list of bools, corresponding to the parameters of (4)
316\\           Pref.Ori.           (list) Preferred Orientation. List of eight parameters.
317                                Items marked SH are only used for Spherical Harmonics.
318                               
319                                0. (str) Type, 'MD' for March-Dollase or 'SH' for Spherical Harmonics
320                                1. (float) Value
321                                2. (bool) Refinement flag
322                                3. (list) Preferred direction, list of ints, [h, k, l]
323                                4. (int) SH - number of terms
324                                5. (dict) SH - 
325                                6. (list) SH
326                                7. (float) SH
327\\           Scale               (list of [float, bool]) Phase fraction & refine flag
328\\           Size                List of crystallite size parameters, in order:
329
330                                0. (str) Type, one of  u'isotropic', u'uniaxial', u'ellipsoidal'
331                                1. (list) Isotropic/uniaxial parameters - list of 3 floats
332                                2. (list) Refinement flags - list of 3 bools
333                                3. (list) Size axis - list of 3 ints, [h, k, l]
334                                4. (list) Ellipsoidal size parameters - list of 6 floats
335                                5. (list) Ellipsoidal refinement flags - list of bools, corresponding to the parameters of (4)
336\\           Use                 (bool) True if this histogram is to be used in refinement
337MCSA            \\               (dict) Monte-Carlo simulated annealing parameters
338==========  ===============     =====================================================================================================
339
340.. _RBData_table:
341
342.. index::
343   single: Rigid Body Data description
344   single: Data object descriptions; Rigid Body Data
345
346Rigid Body Objects
347------------------
348
349Rigid body descriptions are available for two types of rigid bodies: 'Vector'
350and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
351with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
352with defined refinable torsion angles.
353
354.. tabularcolumns:: |l|l|p{4in}|
355
356==========  ===============     ====================================================
357  key         sub-key           explanation
358==========  ===============     ====================================================
359Vector      RBId                (dict of dict) vector rigid bodies
360\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
361\\           RBname              (str) Name assigned by user to rigid body
362\\           VectMag             (list) vector magnitudes in :math:`\\AA`
363\\           rbXYZ               (list of 3 float Cartesian coordinates for Vector rigid body )
364\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
365                                definition, use center of atoms flag
366\\           VectRef             (list of bool refinement flags for VectMag values )
367\\           rbTypes             (list of str) Atom types for each atom in rigid body
368\\           rbVect              (list of lists) Cartesian vectors for each translation used to build rigid body
369\\           useCount            (int) Number of times rigid body is used in any structure
370Residue     RBId                (dict of dict) residue rigid bodies
371\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
372\\           RBname              (str) Name assigned by user to rigid body
373\\           rbXYZ               (list of 3 float) Cartesian coordinates for Residue rigid body
374\\           rbTypes             (list of str) Atom types for each atom in rigid body
375\\           atNames             (list of str) Names of each atom in rigid body (e.g. C1,N2...)
376\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
377                                definition, use center of atoms flag
378\\           rbSeq               (list) Orig,Piv,angle,Riding : definition of internal rigid body
379                                torsion; origin atom (int), pivot atom (int), torsion angle (float),
380                                riding atoms (list of int)
381\\           SelSeq              (int,int) used by SeqSizer to identify objects
382\\           useCount            (int)Number of times rigid body is used in any structure
383RBIds           \\               (dict) unique Ids generated upon creation of each rigid body
384\\           Vector              (list) Ids for each Vector rigid body
385\\           Residue             (list) Ids for each Residue rigid body
386==========  ===============     ====================================================
387
388.. _SGData_table:
389
390.. index::
391   single: Space Group Data description
392   single: Data object descriptions; Space Group Data
393
394Space Group Objects
395-------------------
396
397Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
398and the information is placed in a SGdata object
399which is a dict with these keys. Magnetic ones are marked "mag"
400
401.. tabularcolumns:: |l|p{4.5in}|
402
403==========  ========================================================================================
404  key         explanation
405==========  ========================================================================================
406BNSlattsym  mag - (str) BNS magnetic space group symbol and centering vector
407GenFlg      mag - (list) symmetry generators indices
408GenSym      mag - (list) names for each generator
409MagMom      mag - (list) "time reversals" for each magnetic operator
410MagPtGp     mag - (str) Magnetic point group symbol
411MagSpGrp    mag - (str) Magnetic space group symbol
412OprNames    mag - (list) names for each space group operation
413SGCen       (np.array) Symmetry cell centering vectors. A (n,3) np.array
414            of centers. Will always have at least one row: ``np.array([[0, 0, 0]])``
415SGFixed     (bool) Only True if phase mported from a magnetic cif file
416            then the space group can not be changed by the user because
417            operator set from cif may be nonstandard
418SGGen       (list) generators
419SGGray      (bool) True if space group is a gray group (incommensurate magnetic structures)
420SGInv       (bool) True if centrosymmetric, False if not
421SGLatt      (str)Lattice centering type. Will be one of
422            P, A, B, C, I, F, R
423SGLaue      (str) one of the following 14 Laue classes:
424            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
425            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m
426SGOps       (list) symmetry operations as a list of form
427            ``[[M1,T1], [M2,T2],...]``
428            where :math:`M_n` is a 3x3 np.array
429            and :math:`T_n` is a length 3 np.array.
430            Atom coordinates are transformed where the
431            Asymmetric unit coordinates [X is (x,y,z)]
432            are transformed using
433            :math:`X^\\prime = M_n*X+T_n`
434SGPolax     (str) Axes for space group polarity. Will be one of
435            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
436            'xyz'. In the case where axes are arbitrary
437            '111' is used (P 1, and ?).
438SGPtGrp     (str) Point group of the space group
439SGUniq      unique axis if monoclinic. Will be
440            a, b, or c for monoclinic space groups.
441            Will be blank for non-monoclinic.
442SGSpin      mag - (list) of spin flip operatiors (+1 or -1) for the space group operations
443SGSys       (str) symmetry unit cell: type one of
444            'triclinic', 'monoclinic', 'orthorhombic',
445            'tetragonal', 'rhombohedral', 'trigonal',
446            'hexagonal', 'cubic'
447SSGK1       (list) Superspace multipliers
448SpGrp       (str) space group symbol
449SpnFlp      mag - (list) Magnetic spin flips for every magnetic space group operator
450==========  ========================================================================================
451
452.. _SSGData_table:
453
454.. index::
455   single: Superspace Group Data description
456   single: Data object descriptions; Superspace Group Data
457
458Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
459and the information is placed in a SSGdata object
460which is a dict with these keys:
461
462.. tabularcolumns:: |l|p{4.5in}|
463
464==========  ====================================================
465  key         explanation
466==========  ====================================================
467SSGCen      (list) 4D cell centering vectors [0,0,0,0] at least
468SSGK1       (list) Superspace multipliers
469SSGOps      (list) 4D symmetry operations as [M,T] so that M*x+T = x'
470SSpGrp      (str) superspace group symbol extension to space group
471            symbol, accidental spaces removed
472modQ        (list) modulation/propagation vector
473modSymb     (list of str) Modulation symbols
474==========  ====================================================
475
476
477Phase Information
478--------------------
479
480.. index::
481   single: Phase information record description
482
483Phase information is placed in one of the following keys:
484
485.. tabularcolumns:: |l|p{4.5in}|
486
487==========  ==============================================================
488  key         explanation
489==========  ==============================================================
490General       Overall information about a phase
491Histograms    Information about each histogram linked to the
492              current phase as well as parameters that
493              are defined for each histogram and phase
494              (such as sample peak widths and preferred
495              orientation parameters.
496Atoms         Contains a list of atoms, as described in the
497              :ref:`Atom Records <Atoms_table>` description.
498Drawing       Parameters that determine how the phase is
499              displayed, including a list of atoms to be
500              included, as described in the
501              :ref:`Drawing Atom Records <Drawing_atoms_table>`
502              description
503MCSA          Monte-Carlo simulated annealing parameters
504pId           The index of each phase in the project, numbered
505              starting at 0
506ranId         An int value with a unique value for each phase
507RBModels      A list of dicts with parameters for each
508              rigid body inserted into the current phase,
509              as defined in the
510              :ref:`Rigid Body Insertions <Rigid_Body_Insertions>`.
511              Note that the rigid bodies are defined as
512              :ref:`Rigid Body Objects <RBData_table>`
513RMC           PDF modeling parameters
514Pawley ref    Pawley refinement parameters
515
516==========  ==============================================================
517
518.. _Atoms_table:
519
520.. index::
521   single: Atoms record description
522   single: Data object descriptions; Atoms record
523
524--------------------
525Atom Records
526--------------------
527
528If ``phasedict`` points to the phase information in the data tree, then
529atoms are contained in a list of atom records (list) in
530``phasedict['Atoms']``. Also needed to read atom information
531are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
532which define locations in the atom record, as shown below. Items shown are
533always present; additional ones for macromolecular phases are marked 'mm',
534and those for magnetic structures are marked 'mg'
535
536.. tabularcolumns:: |l|p{4.5in}|
537
538==============      ====================================================
539location            explanation
540==============      ====================================================
541ct-4                mm - (str) residue number
542ct-3                mm - (str) residue name (e.g. ALA)
543ct-2                mm - (str) chain label
544ct-1                (str) atom label
545ct                  (str) atom type
546ct+1                (str) refinement flags; combination of 'F', 'X', 'U', 'M'
547cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
548cx+3                (float) site occupancy
549cx+4,cx+5,cx+6      mg - (list) atom magnetic moment along a,b,c in Bohr magnetons
550cs                  (str) site symmetry
551cs+1                (int) site multiplicity
552cia                 (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
553cia+1               (float) Uiso
554cia+2...cia+7       (6 floats) U11, U22, U33, U12, U13, U23
555atom[cia+8]         (int) unique atom identifier
556
557==============      ====================================================
558
559.. _Drawing_atoms_table:
560
561.. index::
562   single: Drawing atoms record description
563   single: Data object descriptions; Drawing atoms record
564
565----------------------------
566Drawing Atom Records
567----------------------------
568
569If ``phasedict`` points to the phase information in the data tree, then
570drawing atoms are contained in a list of drawing atom records (list) in
571``phasedict['Drawing']['Atoms']``. Also needed to read atom information
572are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
573which define locations in the atom record, as shown below. Items shown are
574always present; additional ones for macromolecular phases are marked 'mm',
575and those for magnetic structures are marked 'mg'
576
577.. tabularcolumns:: |l|p{4.5in}|
578
579==============   ===================================================================================
580location            explanation
581==============   ===================================================================================
582ct-4                mm - (str) residue number
583ct-3                mm - (str) residue name (e.g. ALA)
584ct-2                mm - (str) chain label
585ct-1                (str) atom label
586ct                  (str) atom type
587cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
588cx+3,cx+4,cx+5      mg - (3 floats) atom magnetic moment along a,b,c in Bohr magnetons
589cs-1                (str) Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1')
590cs                  (str) atom drawing style; e.g. 'balls & sticks'
591cs+1                (str) atom label style (e.g. 'name')
592cs+2                (int) atom color (RBG triplet)
593cs+3                (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
594cs+4                (float) Uiso
595cs+5...cs+11        (6 floats) U11, U22, U33, U12, U13, U23
596ci                  (int) unique atom identifier; matches source atom Id in Atom Records
597==============   ===================================================================================
598
599.. _Rigid_Body_Insertions:
600
601----------------------------
602Rigid Body Insertions
603----------------------------
604
605If ``phasedict`` points to the phase information in the data tree, then
606rigid body information is contained in list(s) in
607``phasedict['RBModels']['Residue']`` and/or ``phasedict['RBModels']['Vector']``
608for each rigid body inserted into the current phase.
609
610.. tabularcolumns:: |l|p{4.5in}|
611
612==============   ===================================================================================
613key              explanation
614==============   ===================================================================================
615fixOrig           Should the origin be fixed (when editing, not the refinement flag)
616Ids               Ids for assignment of atoms in the rigid body
617numChain          Chain number for macromolecular fits
618Orient            Orientation of the RB as a quaternion and a refinement flag (' ', 'A' or 'AV')
619OrientVec         Orientation of the RB expressed as a vector and azimuthal rotation angle
620Orig              Origin of the RB in fractional coordinates and refinement flag (bool)
621RBId              References the unique ID of a rigid body in the
622                  :ref:`Rigid Body Objects <RBData_table>`
623RBname            The name for the rigid body (str)
624AtomFrac          The atom fractions for the rigid body
625ThermalMotion     The thermal motion description for the rigid body, which includes a choice for
626                  the model and can include TLS parameters or an overall Uiso value.
627Torsions          Defines the torsion angle and refinement flag for each torsion defined in
628                  the :ref:`Rigid Body Object <RBData_table>`
629==============   ===================================================================================
630
631.. _Powder_table:
632
633.. index::
634   single: Powder data object description
635   single: Data object descriptions; Powder Data
636
637Powder Diffraction Tree Items
638-----------------------------
639
640Every powder diffraction histogram is stored in the GSAS-II data tree
641with a top-level entry named beginning with the string "PWDR ". The
642diffraction data for that information are directly associated with
643that tree item and there are a series of children to that item. The
644routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
645and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
646load this information into a dictionary where the child tree name is
647used as a key, and the information in the main entry is assigned
648a key of ``Data``, as outlined below.
649
650.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
651
652======================     ===============  ===========================================================
653  key                       sub-key          explanation
654======================     ===============  ===========================================================
655Comments                    \\               (list of str) Text strings extracted from the original powder
656                                            data header. These cannot be changed by the user;
657                                            it may be empty.
658Limits                      \\               (list) two two element lists, as [[Ld,Hd],[L,H]]
659                                            where L and Ld are the current and default lowest
660                                            two-theta value to be used and
661                                            where H and Hd are the current and default highest
662                                            two-theta value to be used.
663Reflection Lists            \\               (dict of dicts) with an entry for each phase in the
664                                            histogram. The contents of each dict item
665                                            is a dict containing reflections, as described in
666                                            the :ref:`Powder Reflections <PowderRefl_table>`
667                                            description.
668Instrument Parameters       \\               (dict) The instrument parameters uses different dicts
669                                            for the constant wavelength (CW) and time-of-flight (TOF)
670                                            cases. See below for the descriptions of each.
671wtFactor                    \\               (float) A weighting factor to increase or decrease
672                                            the leverage of data in the histogram .
673                                            A value of 1.0 weights the data with their
674                                            standard uncertainties and a larger value
675                                            increases the weighting of the data (equivalent
676                                            to decreasing the uncertainties).
677Sample Parameters           \\               (dict) Parameters that describe how
678                                            the data were collected, as listed
679                                            below. Refinable parameters are a list containing
680                                            a float and a bool, where the second value
681                                            specifies if the value is refined, otherwise
682                                            the value is a float unless otherwise noted.
683\\                           Scale           The histogram scale factor (refinable)
684\\                           Absorption      The sample absorption coefficient as
685                                            :math:`\\mu r` where r is the radius
686                                            (refinable). Only valid for Debye-Scherrer geometry.
687\\                           SurfaceRoughA   Surface roughness parameter A as defined by
688                                            Surotti, *J. Appl. Cryst*, **5**, 325-331, 1972.
689                                            (refinable - only valid for Bragg-Brentano geometry)
690\\                           SurfaceRoughB   Surface roughness parameter B (refinable -
691                                            only valid for Bragg-Brentano geometry)
692\\                           DisplaceX,      Sample displacement from goniometer center
693                            DisplaceY       where Y is along the beam direction and
694                                            X is perpendicular. Units are :math:`\\mu m`
695                                            (refinable).
696\\                           Phi, Chi,       Goniometer sample setting angles, in degrees.
697                            Omega
698\\                           Gonio. radius   Radius of the diffractometer in mm
699\\                           InstrName       (str) A name for the instrument, used in preparing
700                                            a CIF .
701\\                           Force,          Variables that describe how the measurement
702                            Temperature,    was performed. Not used directly in
703                            Humidity,       any computations.
704                            Pressure,
705                            Voltage
706\\                           ranId           (int) The random-number Id for the histogram
707                                            (same value as where top-level key is ranId)
708\\                           Type            (str) Type of diffraction data, may be 'Debye-Scherrer'
709                                            or 'Bragg-Brentano' .
710hId                         \\               (int) The number assigned to the histogram when
711                                            the project is loaded or edited (can change)
712ranId                       \\               (int) A random number id for the histogram
713                                            that does not change
714Background                  \\               (list) The background is stored as a list with where
715                                            the first item in the list is list and the second
716                                            item is a dict. The list contains the background
717                                            function and its coefficients; the dict contains
718                                            Debye diffuse terms and background peaks.
719                                            (TODO: this needs to be expanded.)
720Data                        \\               (list) The data consist of a list of 6 np.arrays
721                                            containing in order:
722
723                                            0. the x-postions (two-theta in degrees),
724                                            1. the intensity values (Yobs),
725                                            2. the weights for each Yobs value
726                                            3. the computed intensity values (Ycalc)
727                                            4. the background values
728                                            5. Yobs-Ycalc
729======================     ===============  ===========================================================
730
731.. _CWPowder_table:
732
733.. index::
734   single: Powder data CW Instrument Parameters
735
736-----------------------------
737CW Instrument Parameters
738-----------------------------
739
740Instrument Parameters are placed in a list of two dicts,
741where the keys in the first dict are listed below. Note that the dict contents are different for
742constant wavelength (CW) vs. time-of-flight (TOF) histograms.
743The value for each item is a list containing three values: the initial value, the current value
744and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
745cannot be refined. The first and second values are floats unless otherwise noted.
746Items not refined are noted as [*]
747
748.. tabularcolumns:: |l|p{1in}|p{4in}|
749
750========================    ===============  ===========================================================
751  key                       sub-key           explanation
752========================    ===============  ===========================================================
753Instrument Parameters[0]    Type [*]            (str) Histogram type:
754                                                * 'PXC' for constant wavelength x-ray
755                                                * 'PNC' for constant wavelength neutron
756\\                           Bank [*]            (int) Data set number in a multidata file (usually 1)
757\\                           Lam                 (float) Specifies a wavelength in :math:`\\AA`
758\\                           Lam1 [*]            (float) Specifies the primary wavelength in
759                                                :math:`\\AA`, used in place of Lam
760                                                when an :math:`\\alpha_1, \\alpha_2`
761                                                source is used.
762\\                           Lam2 [*]            (float) Specifies the secondary wavelength in
763                                                :math:`\\AA`, used with Lam1
764\\                           I(L2)/I(L1)         (float) Ratio of Lam2 to Lam1, used with Lam1
765\\                           Zero                (float) Two-theta zero correction in *degrees*
766\\                           Azimuth [*]         (float) Azimuthal setting angle for data recorded with differing setting angles
767\\                           U, V, W             (float) Cagliotti profile coefficients
768                                                for Gaussian instrumental broadening, where the
769                                                FWHM goes as
770                                                :math:`U \\tan^2\\theta + V \\tan\\theta + W`
771\\                           X, Y, Z             (float) Cauchy (Lorentzian) instrumental broadening coefficients
772\\                           SH/L                (float) Variant of the Finger-Cox-Jephcoat asymmetric
773                                                peak broadening ratio. Note that this is the
774                                                sum of S/L and H/L where S is
775                                                sample height, H is the slit height and
776                                                L is the goniometer diameter.
777\\                           Polariz.            (float) Polarization coefficient.
778Instrument Parameters[1]                        (empty dict)
779========================    ===============  ===========================================================
780
781.. _TOFPowder_table:
782
783.. index::
784   single: Powder data TOF Instrument Parameters
785
786-----------------------------
787TOF Instrument Parameters
788-----------------------------
789
790Instrument Parameters are also placed in a list of two dicts,
791where the keys in each dict listed below, but here for
792time-of-flight (TOF) histograms.
793The value for each item is a list containing three values: the initial value, the current value
794and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
795cannot be refined. The first and second values are floats unless otherwise noted.
796Items not refined are noted as [*]
797
798.. tabularcolumns:: |l|p{1.5in}|p{4in}|
799
800========================    ===============  ===========================================================
801  key                        sub-key          explanation
802========================    ===============  ===========================================================
803Instrument Parameters[0]    Type [*]            (str) Histogram type:
804                                                * 'PNT' for time of flight neutron
805\\                           Bank                (int) Data set number in a multidata file
806\\                           2-theta [*]         (float) Nominal scattering angle for the detector
807\\                           fltPath [*]         (float) Total flight path source-sample-detector
808\\                           Azimuth [*]         (float) Azimuth angle for detector right hand rotation
809                                                from horizontal away from source
810\\                           difC,difA,          (float) Diffractometer constants for conversion of d-spacing to TOF
811                            difB                in microseconds
812\\                           Zero                (float) Zero point offset (microseconds)
813\\                           alpha               (float) Exponential rise profile coefficients
814\\                           beta-0              (float) Exponential decay profile coefficients
815                            beta-1
816                            beta-q
817\\                           sig-0               (float) Gaussian profile coefficients
818                            sig-1
819                            sig-2
820                            sig-q   
821\\                           X,Y,Z               (float) Lorentzian profile coefficients
822Instrument Parameters[1]    Pdabc               (list of 4 float lists) Originally created for use in gsas as optional tables
823                                                of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation
824                                                from the d-spacing and these tables. The d-true column is apparently unused.
825========================    ===============  ===========================================================
826
827
828.. _PowderRefl_table:
829
830.. index::
831   single: Powder reflection object description
832   single: Data object descriptions; Powder Reflections
833
834Powder Reflection Data Structure
835--------------------------------
836
837For every phase in a histogram, the ``Reflection Lists`` value is a dict
838one element of which is `'RefList'`, which is a np.array containing
839reflections. The columns in that array are documented below.
840
841==========  ====================================================
842  index         explanation
843==========  ====================================================
844 0,1,2          h,k,l (float)
845 3              (int) multiplicity
846 4              (float) d-space, :math:`\\AA`
847 5              (float) pos, two-theta
848 6              (float) sig, Gaussian width
849 7              (float) gam, Lorenzian width
850 8              (float) :math:`F_{obs}^2`
851 9              (float) :math:`F_{calc}^2`
852 10             (float) reflection phase, in degrees
853 11             (float) intensity correction for reflection, this times
854                :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
855 12             (float) Preferred orientation correction
856 13             (float) Transmission (absorption correction)
857 14             (float) Extinction correction
858==========  ====================================================
859
860.. _Xtal_table:
861
862.. index::
863   single: Single Crystal data object description
864   single: Data object descriptions; Single crystal data
865
866Single Crystal Tree Items
867-------------------------
868
869Every single crystal diffraction histogram is stored in the GSAS-II data tree
870with a top-level entry named beginning with the string "HKLF ". The
871diffraction data for that information are directly associated with
872that tree item and there are a series of children to that item. The
873routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
874and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
875load this information into a dictionary where the child tree name is
876used as a key, and the information in the main entry is assigned
877a key of ``Data``, as outlined below.
878
879.. tabularcolumns:: |l|l|p{4in}|
880
881======================  ===============     ====================================================
882  key                      sub-key          explanation
883======================  ===============     ====================================================
884Data                        \\               (dict) that contains the
885                                            reflection table,
886                                            as described in the
887                                            :ref:`Single Crystal Reflections
888                                            <XtalRefl_table>`
889                                            description.
890
891Instrument Parameters       \\               (list) containing two dicts where the possible
892                                            keys in each dict are listed below. The value
893                                            for most items is a list containing two values:
894                                            the initial value, the current value.
895                                            The first and second
896                                            values are floats unless otherwise noted.
897\\                           Lam             (two floats) Specifies a wavelength in :math:`\\AA`
898\\                           Type            (two str values) Histogram type :
899                                            * 'SXC' for constant wavelength x-ray
900                                            * 'SNC' for constant wavelength neutron
901                                            * 'SNT' for time of flight neutron
902\\                           InstrName       (str) A name for the instrument, used in preparing a CIF
903wtFactor                    \\               (float) A weighting factor to increase or decrease
904                                            the leverage of data in the histogram.
905                                            A value of 1.0 weights the data with their
906                                            standard uncertainties and a larger value
907                                            increases the weighting of the data (equivalent
908                                            to decreasing the uncertainties).
909
910hId                         \\               (int) The number assigned to the histogram when
911                                            the project is loaded or edited (can change)
912ranId                       \\               (int) A random number id for the histogram
913                                            that does not change
914======================  ===============     ====================================================
915
916.. _XtalRefl_table:
917
918.. index::
919   single: Single Crystal reflection object description
920   single: Data object descriptions; Single Crystal Reflections
921
922Single Crystal Reflection Data Structure
923----------------------------------------
924
925For every single crystal a histogram, the ``'Data'`` item contains
926the structure factors as an np.array in item `'RefList'`.
927The columns in that array are documented below.
928
929.. tabularcolumns:: |l|p{4in}|
930
931==========  ====================================================
932  index         explanation
933==========  ====================================================
934 0,1,2          (float) h,k,l
935 3              (int) multiplicity
936 4              (float) d-space, :math:`\\AA`
937 5              (float) :math:`F_{obs}^2`
938 6              (float) :math:`\\sigma(F_{obs}^2)`
939 7              (float) :math:`F_{calc}^2`
940 8              (float) :math:`F_{obs}^2T`
941 9              (float) :math:`F_{calc}^2T`
942 10             (float) reflection phase, in degrees
943 11             (float) intensity correction for reflection, this times
944                :math:`F_{obs}^2` or :math:`F_{calc}^2`
945                gives Iobs or Icalc
946==========  ====================================================
947
948.. _Image_table:
949
950.. index::
951   image: Image data object description
952   image: Image object descriptions
953
954Image Data Structure
955--------------------
956
957Every 2-dimensional image is stored in the GSAS-II data tree
958with a top-level entry named beginning with the string "IMG ". The
959image data are directly associated with that tree item and there
960are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
961and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
962load this information into a dictionary where the child tree name is
963used as a key, and the information in the main entry is assigned
964a key of ``Data``, as outlined below.
965
966.. tabularcolumns:: |l|l|p{4in}|
967
968======================  ======================  ====================================================
969  key                      sub-key              explanation
970======================  ======================  ====================================================
971Comments                    \\                   (list of str) Text strings extracted from the original image data
972                                                header or a metafile. These cannot be changed by
973                                                the user; it may be empty.
974Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
975                                                value. Accomodates
976                                                detector orientations other than with the detector
977                                                X-axis
978                                                horizontal.
979\\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
980                                                during image integration multiplied by value. It must have the same size/shape as
981                                                the integrated image. NB: value < 0 for subtraction.
982\\                           calibrant           (str) The material used for determining the position/orientation
983                                                of the image. The data is obtained from :func:`ImageCalibrants`
984                                                and UserCalibrants.py (supplied by user).
985\\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
986\\                           calibskip           (int) The number of expected diffraction lines skipped during the last
987                                                calibration run.
988\\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
989                                                strikes the detector plane as determined by calibration. This point
990                                                does not have to be within the limits of the detector boundaries.
991\\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
992                                                of the image is at the center line otherwise it is at the leading edge.
993\\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
994\\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
995                                                calibration calculations. See pixLimit for details as how point is found.
996\\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
997                                                ring offset at higher angles. Optionally determined by calibration.
998\\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
999\\                           distance            (float) The distance (mm) from sample to detector plane.
1000\\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
1001                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
1002                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
1003                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
1004                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
1005\\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
1006\\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
1007\\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
1008                                                Required for texture calculations.
1009\\                           invert_x            (bool) If True display the image with the x-axis inverted.
1010\\                           invert_y            (bool) If True display the image with the y-axis inverted.
1011\\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
1012\\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
1013\\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
1014                                                intensities obtained during integration.
1015\\                           outAzimuths         (int) The number of azimuth pie slices.
1016\\                           outChannels         (int) The number of 2-theta steps.
1017\\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
1018\\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
1019                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
1020                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
1021                                                Locations are used to construct rings of points for calibration calcualtions.
1022\\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
1023                                                integration using value.
1024\\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
1025                                                diffraction ring with the same d-spacing (dsp)
1026\\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
1027                                                selected by the user,
1028\\                           Range               (list) The minimum & maximum values of the image
1029\\                           rotation            (float) The angle between the x-axis and the vector about which the
1030                                                detector is tilted. Constrained to -180 to 180 deg.
1031\\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
1032                                                calculations.
1033\\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
1034                                                to cause correction to be applied.
1035\\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
1036\\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
1037\\                           showLines           (bool) If True then isplay the integration limits to be used.
1038\\                           size                (list:int) The number of pixels on the image x & y axes
1039\\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
1040\\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
1041\\                           wavelength          (float) The radiation wavelength (:math:`\\AA`) as entered by the user
1042                                                (or someday obtained from the image header).
1043Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
1044                                                to be excluded from integration
1045\\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
1046                                                of which is excluded from recalibration and integration. Only one frame is allowed.
1047\\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
1048                                                from integration.
1049\\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
1050                                                to be excluded from integration.
1051\\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
1052                                                to be excluded from integration.
1053\\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
1054                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
1055\\                           SpotMask            (dict: int & array)
1056                                                'esdMul'(int) number of standard deviations above mean ring intensity to mask
1057                                                'spotMask' (bool array) the spot mask for every pixel in image         
1058
1059Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
1060\\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
1061                                                These will be restricted by space group symmetry; result of strain fit refinement.
1062\\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
1063\\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
1064                                                and are used to determine the strain tensor.
1065                                                The dictionary items are:
1066                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
1067                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
1068                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
1069                                                'Esig': (list: float) Esds for Emat from fitting.
1070                                                'pixLimit': (int) Search range to find highest point on ring for each data point
1071                                                'cutoff': (float) I/Ib cutoff for searching.
1072                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
1073                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
1074                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
1075
1076======================  ======================  ====================================================
1077
1078.. _parmDict_table:
1079
1080.. index::
1081   single: Parameter dictionary
1082
1083Parameter Dictionary
1084-------------------------
1085
1086The parameter dictionary contains all of the variable parameters for the refinement.
1087The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
1088It is prepared in two ways. When loaded from the tree
1089(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
1090:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
1091the values are lists with two elements: ``[value, refine flag]``
1092
1093When loaded from the GPX file (in
1094:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
1095dict is the actual parameter value (usually a float, but sometimes a
1096letter or string flag value (such as I or A for iso/anisotropic).
1097
1098Texture implementation
1099------------------------------
1100
1101There are two different places where texture can be treated in GSAS-II.
1102One is for mitigating the effects of texture in a structural refinement.
1103The other is for texture characterization.
1104
1105For reducing the effect of texture in a structural refinement
1106there are entries labeled preferred orientation in each phase's
1107data tab. Two different approaches can be used for this, the March-Dollase
1108model and spherical harmonics.
1109
1110For the March-Dollase model, one axis in reciprocal space is designated as
1111unique (defaulting to the 001 axis) and reflections are corrected
1112according to the angle they make with this axis depending on
1113the March-Dollase ratio. (If unity, no correction is made).
1114The ratio can be greater than one or less than one depending on if
1115crystallites oriented along the designated axis are
1116overrepresented or underrepresented. For most crystal systems there is an
1117obvious choice for the direction of the unique axis and then only a single
1118term needs to be refined. If the number is close to 1, then the correction
1119is not needed.
1120
1121The second method for reducing the effect of texture in a structural
1122refinement is to create a crystallite orientation probability surface as an
1123expansion in terms spherical harmonic functions. Only functions consistent with
1124cylindrical diffraction suymmetry and having texture symmetry
1125consistent with the Laue class of phase are used and are allowed,
1126so the higher the symmetry the fewer terms that are available for a given spherical harmonics order.
1127To use this correction, select the lowest order that provides
1128refinable terms and perform a refinement. If the texture index remains close to
1129one, then the correction is not needed. If a significant improvement is
1130noted in the profile Rwp, one may wish to see if a higher order expansion
1131gives an even larger improvement.
1132
1133To characterize texture in a material, generally one needs data collected with the
1134sample at multiple orientations or, for TOF, with detectors at multiple
1135locations around the sample. In this case the detector orientation is given in
1136each histogram's Sample Parameters and the sample's orientation is described
1137with the Euler angles specifed on the phase's Texture tab, which is also
1138where the texture type (cylindrical, rolling,...) and the spherical
1139harmonic order is selected. This should not be used with a single dataset and
1140should not be used if the preferred orientations corrections are used.
1141
1142The coordinate system used for texture characterization is defined where
1143the sample coordinates (Psi, gamma) are defined with an instrument coordinate
1144system (I, J, K) such that K is normal to the diffraction plane and J is coincident with the
1145direction of the incident radiation beam toward the source. We further define
1146a standard set of right-handed goniometer eulerian angles (Omega, Chi, Phi) so that Omega and Phi are
1147rotations about K and Chi is a rotation about J when Omega = 0. Finally, as the sample
1148may be mounted so that the sample coordinate system (Is, Js, Ks) does not coincide with
1149the instrument coordinate system (I, J, K), we define three eulerian sample rotation angles
1150(Omega-s, Chi-s, Phi-s) that describe the rotation from (Is, Js, Ks) to (I, J, K). The sample rotation
1151angles are defined so that with the goniometer angles at zero Omega-s and Phi-s are rotations
1152about K and Chi-s is a rotation about J.
1153
1154Three typical examples:
1155
1156    1) Bragg-Brentano laboratory diffractometer: Chi=0
1157    2) Debye-Scherrer counter detector; sample capillary axis perpendicular to diffraction plane: Chi=90
1158    3) Debye-Scherrer 2D area detector positioned directly behind sample; sample capillary axis horizontal; Chi=0
1159
1160NB: The area detector azimuthal angle will equal 0 in horizontal plane to right as viewed from x-ray source and will equal
116190 at vertical "up" direction.
1162           
1163ISODISTORT implementation
1164------------------------------
1165
1166CIFs prepared with the ISODISTORT web site
1167https://stokes.byu.edu/iso/isodistort_version5.6.1/isodistort.php
1168[B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions."
1169J. Appl. Cryst. 39, 607-614 (2006).] can be read into GSAS-II using import CIF. This will cause constraints to be established for
1170structural distortion modes read from the CIF. At present, of the five types of modes  only displacive(``_iso_displacivemode``...)
1171and occupancy (``_iso_occupancymode``...) are processed. Not yet processed: ``_iso_magneticmode``...,
1172``_iso_rotationalmode``... & ``_iso_strainmode``...
1173
1174The CIF importer :mod:`G2phase_CIF` implements class :class:`G2phase_CIF.CIFPhaseReader` which offers two methods associated
1175with ISODISTORT (ID) input. Method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_test` checks to see if a CIF block contains
1176the loops with ``_iso_displacivemode_label`` or  ``_iso_occupancymode_label`` items. If so, method
1177:meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_proc` is called to read and interpret them. The results are placed into the
1178reader object's ``.Phase`` class variable as a dict item with key ``'ISODISTORT'``.
1179
1180Note 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
1181:func:`G2phase_CIF.ISODISTORT_shortLbl` is used to create a short name for this, such as R5_T1u(a) which is made unique
1182by addition of _n if the short name is duplicated. As each mode is processed, a constraint corresponding to that mode is
1183created and is added to list in the reader object's ``.Constraints`` class variable. Items placed into that list can either
1184be a list, which corresponds to a function (new var) type :ref:`constraint definition <Constraints_table>` entry, or an item
1185can be a dict, which provides help information for each constraint.
1186
1187------------------------------
1188Displacive modes
1189------------------------------
1190
1191The coordinate variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoVarList']`` and the
1192corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2VarList']``.
1193The mode variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoModeList']`` and the
1194corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2ModeList']``.
1195[Use ``str(G2VarObj)`` to get the variable name from the G2VarObj object, but note that the phase number, *n*, for the prefix
1196"*n*::" cannot be determined as the phase number is not yet assigned.]
1197
1198Displacive modes are a bit complex in that they relate to delta displacements, relative to an offset value for each coordinate,
1199and because the modes are normalized. While GSAS-II also uses displacements,  these are added to the coordinates after
1200each refinement cycle and then the delta values are set to zero.
1201ISODISTORT uses fixed offsets (subtracted from the actual position
1202to obtain the delta values) that are taken from the parent structure coordinate and the initial offset value
1203(in ``_iso_deltacoordinate_value``) and these are placed in
1204``.Phase['ISODISTORT']['G2coordOffset']`` in the same order as ``.Phase['ISODISTORT']['G2ModeList']``,
1205``.Phase['ISODISTORT']['IsoVarList']`` and ''.Phase[ISODISTORT']['G2parentCoords']''.'
1206
1207The normalization factors (which the delta values are divided by)
1208are taken from ``_iso_displacivemodenorm_value`` and are placed in ``.Phase['ISODISTORT']['NormList']`` in the same
1209order as as ``...['IsoModeList']`` and ``...['G2ModeList']``.
1210
1211The CIF contains a sparse matrix, from the ``loop_`` containing ``_iso_displacivemodematrix_value`` which provides the equations
1212for determining the mode values from the coordinates, that matrix is placed in ``.Phase['ISODISTORT']['Mode2VarMatrix']``.
1213The matrix is inverted to produce ``.Phase['ISODISTORT']['Var2ModeMatrix']``, which determines how to compute the
1214mode values from the delta coordinate values. These values are used for the in :func:`GSASIIconstrGUI.ShowIsoDistortCalc`,
1215which shows coordinate and mode values, the latter with s.u. values.
1216
1217------------------------------
1218Occupancy modes
1219------------------------------
1220
1221
1222The delta occupancy variables, as named by ISODISTORT, are placed in
1223``.Phase['ISODISTORT']['OccVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed
1224in ``.Phase['ISODISTORT']['G2OccVarList']``. The mode variables, as named by ISODISTORT, are placed in
1225``.Phase['ISODISTORT']['OccModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed
1226in ``.Phase['ISODISTORT']['G2OccModeList']``.
1227
1228Occupancy modes, like Displacive modes, are also refined as delta values.  However, GSAS-II directly refines the fractional
1229occupancies. Offset values for each atom, are taken from ``_iso_occupancy_formula`` and are placed in
1230``.Phase['ISODISTORT']['ParentOcc]``. (Offset values are subtracted from the actual position to obtain the delta values.)
1231Modes are normalized (where the mode values are divided by the normalization factor) are taken from ``_iso_occupancymodenorm_value``
1232and are placed in ``.Phase['ISODISTORT']['OccNormList']`` in the same order as as ``...['OccModeList']`` and
1233``...['G2OccModeList']``.
1234
1235The CIF contains a sparse matrix, from the ``loop_`` containing ``_iso_occupancymodematrix_value``, which provides the
1236equations for determining the mode values from the coordinates. That matrix is placed in ``.Phase['ISODISTORT']['Occ2VarMatrix']``.
1237The matrix is inverted to produce ``.Phase['ISODISTORT']['Var2OccMatrix']``, which determines how to compute the
1238mode values from the delta coordinate values.
1239
1240
1241------------------------------
1242Mode Computations
1243------------------------------
1244
1245Constraints are processed after the CIF has been read in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` or 
1246:meth:`GSASIIscriptable.G2Project.add_phase` by moving them from the reader object's ``.Constraints``
1247class variable to the Constraints tree entry's ['Phase'] list (for list items defining constraints) or
1248the Constraints tree entry's ['_Explain'] dict (for dict items defining constraint help information)
1249
1250The information in ``.Phase['ISODISTORT']`` is used in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1251values, the latter with s.u. values. This can be called from the Constraints and Phase/Atoms tree items.
1252
1253Before each refinement, constraints are processed as :ref:`described elsewhere <Constraints_processing>`. After a refinement
1254is complete, :func:`GSASIImapvars.PrintIndependentVars` shows the shifts and s.u.'s on the refined modes,
1255using GSAS-II values, but :func:`GSASIIstrIO.PrintISOmodes` prints the ISODISTORT modes as computed in the web site.
1256
1257
1258.. _ParameterLimits:
1259
1260.. index::
1261   single: Parameter limits
1262
1263Parameter Limits
1264------------------------------
1265
1266One of the most often requested "enhancements" for GSAS-II would be the inclusion
1267of constraints to force parameters such as occupancies or Uiso values to stay within
1268expected ranges. While it is possible for users to supply their own restraints that would
1269perform this by supplying an appropriate expression with the "General" restraints, the
1270GSAS-II authors do not feel that use of restraints or constraints are a good solution for
1271this common problem where parameters refine to non-physical values. This is because when
1272this occurs, most likely one of the following cases is occurring:
1273
1274#. there is a significant problem
1275   with the model, for example for an x-ray fit if an O atom is placed where a S is actually
1276   present, the Uiso will refine artificially small or the occupancy much larger than unity
1277   to try to compensate for the missing electrons; or
1278 
1279#. the data are simply insensitive
1280   to the parameter or combination of parameters, for example unless very high-Q data
1281   are included, the effects of a occupancy and Uiso value can have compensating effects,
1282   so an assumption must be made; likewise, with neutron data natural-abundance V atoms
1283   are nearly invisible due to weak coherent scattering. No parameters can be fit for a
1284   V atom with neutrons.
1285
1286#. the parameter is non-physical (such as a negative Uiso value) but within
1287   two sigma (sigma = standard uncertainty, aka e.s.d.) of a reasonable value,
1288   in which case the
1289   value is not problematic as it is experimentally indistinguishable from an
1290   expected value. 
1291
1292#. there is a systematic problem with the data (experimental error)
1293
1294In all these cases, this situation needs to be reviewed by a crystallographer to decide
1295how to best determine a structural model for these data. An implementation with a constraint
1296or restraint is likely to simply hide the problem from the user, making it more probable
1297that a poor model choice is obtained.
1298
1299What GSAS-II does implement is to allow users to specify ranges for parameters
1300that works by disabling
1301refinement of parameters that refine beyond either a lower limit or an upper limit, where
1302either or both may be optionally specified. Parameters limits are specified in the Controls
1303tree entry in dicts named as ``Controls['parmMaxDict']`` and ``Controls['parmMinDict']``, where
1304the keys are :class:`G2VarObj` objects corresponding to standard GSAS-II variable
1305(see :func:`getVarDescr` and :func:`CompileVarDesc`) names, where a
1306wildcard ('*') may optionally be used for histogram number or atom number
1307(phase number is intentionally not  allowed as a wildcard as it makes little sense
1308to group the same parameter together different phases). Note
1309that :func:`prmLookup` is used to see if a name matches a wildcard. The upper or lower limit
1310is placed into these dicts as a float value. These values can be edited using the window
1311created by the Calculate/"View LS parms" menu command or in scripting with the
1312:meth:`GSASIIscriptable.G2Project.set_Controls` function.
1313In the GUI, a checkbox labeled "match all histograms/atoms" is used to insert a wildcard
1314into the appropriate part of the variable name.
1315
1316When a refinement is conducted, routine :func:`GSASIIstrMain.dropOOBvars` is used to
1317find parameters that have refined to values outside their limits. If this occurs, the parameter
1318is set to the limiting value and the variable name is added to a list of frozen variables
1319(as a :class:`G2VarObj` objects) kept in a list in the
1320``Controls['parmFrozen']`` dict. In a sequential refinement, this is kept separate for
1321each histogram as a list in
1322``Controls['parmFrozen'][histogram]`` (where the key is the histogram name) or as a list in
1323``Controls['parmFrozen']['FrozenList']`` for a non-sequential fit.
1324This allows different variables
1325to be frozen in each section of a sequential fit.
1326Frozen parameters are not included in refinements through removal from the
1327list of parameters to be refined (``varyList``) in :func:`GSASIIstrMain.Refine` or
1328:func:`GSASIIstrMain.SeqRefine`.
1329The data window for the Controls tree item shows the number of Frozen variables and
1330the individual variables can be viewed with the Calculate/"View LS parms" menu window or
1331obtained with :meth:`GSASIIscriptable.G2Project.get_Frozen`.
1332Once a variable is frozen, it will not be refined in any
1333future refinements unless the the variable is removed (manually) from the list. This can also
1334be done with the Calculate/"View LS parms" menu window or
1335:meth:`GSASIIscriptable.G2Project.set_Frozen`.
1336
1337
1338.. seealso::
1339  :class:`G2VarObj`
1340  :func:`getVarDescr`
1341  :func:`CompileVarDesc`
1342  :func:`prmLookup`
1343  :class:`GSASIIctrlGUI.ShowLSParms`
1344  :class:`GSASIIctrlGUI.VirtualVarBox`
1345  :func:`GSASIIstrIO.SetUsedHistogramsAndPhases`
1346  :func:`GSASIIstrIO.SaveUpdatedHistogramsAndPhases`
1347  :func:`GSASIIstrIO.SetSeqResult`
1348  :func:`GSASIIstrMain.dropOOBvars`
1349  :meth:`GSASIIscriptable.G2Project.set_Controls`
1350  :meth:`GSASIIscriptable.G2Project.get_Frozen`
1351  :meth:`GSASIIscriptable.G2Project.set_Frozen`
1352
1353*Classes and routines*
1354----------------------
1355
1356'''
1357from __future__ import division, print_function
1358import platform
1359import re
1360import random as ran
1361import sys
1362import os.path
1363if '2' in platform.python_version_tuple()[0]:
1364    import cPickle
1365else:
1366    import pickle as cPickle
1367import GSASIIpath
1368import GSASIImath as G2mth
1369import GSASIIspc as G2spc
1370import numpy as np
1371
1372GSASIIpath.SetVersionNumber("$Revision: 5148 $")
1373
1374DefaultControls = {
1375    'deriv type':'analytic Hessian',
1376    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
1377    'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
1378    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
1379    'Author':'no name','newLeBail':False,
1380    'FreePrm1':'Sample humidity (%)',
1381    'FreePrm2':'Sample voltage (V)',
1382    'FreePrm3':'Applied load (MN)',
1383    'ShowCell':False,
1384    }
1385'''Values to be used as defaults for the initial contents of the ``Controls``
1386data tree item.
1387'''
1388def StripUnicode(string,subs='.'):
1389    '''Strip non-ASCII characters from strings
1390
1391    :param str string: string to strip Unicode characters from
1392    :param str subs: character(s) to place into string in place of each
1393      Unicode character. Defaults to '.'
1394
1395    :returns: a new string with only ASCII characters
1396    '''
1397    s = ''
1398    for c in string:
1399        if ord(c) < 128:
1400            s += c
1401        else:
1402            s += subs
1403    return s
1404#    return s.encode('ascii','replace')
1405
1406def MakeUniqueLabel(lbl,labellist):
1407    '''Make sure that every a label is unique against a list by adding
1408    digits at the end until it is not found in list.
1409
1410    :param str lbl: the input label
1411    :param list labellist: the labels that have already been encountered
1412    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
1413      ``_10-99``, etc.) appended at the end
1414    '''
1415    lbl = StripUnicode(lbl.strip(),'_')
1416    if not lbl: # deal with a blank label
1417        lbl = '_1'
1418    if lbl not in labellist:
1419        labellist.append(lbl)
1420        return lbl
1421    i = 1
1422    prefix = lbl
1423    if '_' in lbl:
1424        prefix = lbl[:lbl.rfind('_')]
1425        suffix = lbl[lbl.rfind('_')+1:]
1426        try:
1427            i = int(suffix)+1
1428        except: # suffix could not be parsed
1429            i = 1
1430            prefix = lbl
1431    while prefix+'_'+str(i) in labellist:
1432        i += 1
1433    else:
1434        lbl = prefix+'_'+str(i)
1435        labellist.append(lbl)
1436    return lbl
1437
1438PhaseIdLookup = {}
1439'''dict listing phase name and random Id keyed by sequential phase index as a str;
1440best to access this using :func:`LookupPhaseName`
1441'''
1442PhaseRanIdLookup = {}
1443'''dict listing phase sequential index keyed by phase random Id;
1444best to access this using :func:`LookupPhaseId`
1445'''
1446HistIdLookup = {}
1447'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
1448best to access this using :func:`LookupHistName`
1449'''
1450HistRanIdLookup = {}
1451'''dict listing histogram sequential index keyed by histogram random Id;
1452best to access this using :func:`LookupHistId`
1453'''
1454AtomIdLookup = {}
1455'''dict listing for each phase index as a str, the atom label and atom random Id,
1456keyed by atom sequential index as a str;
1457best to access this using :func:`LookupAtomLabel`
1458'''
1459AtomRanIdLookup = {}
1460'''dict listing for each phase the atom sequential index keyed by atom random Id;
1461best to access this using :func:`LookupAtomId`
1462'''
1463ShortPhaseNames = {}
1464'''a dict containing a possibly shortened and when non-unique numbered
1465version of the phase name. Keyed by the phase sequential index.
1466'''
1467ShortHistNames = {}
1468'''a dict containing a possibly shortened and when non-unique numbered
1469version of the histogram name. Keyed by the histogram sequential index.
1470'''
1471
1472#VarDesc = {}  # removed 1/30/19 BHT as no longer needed (I think)
1473#''' This dictionary lists descriptions for GSAS-II variables,
1474#as set in :func:`CompileVarDesc`. See that function for a description
1475#for how keys and values are written.
1476#'''
1477
1478reVarDesc = {}
1479''' This dictionary lists descriptions for GSAS-II variables where
1480keys are compiled regular expressions that will match the name portion
1481of a parameter name. Initialized in :func:`CompileVarDesc`.
1482'''
1483
1484reVarStep = {}
1485''' This dictionary lists the preferred step size for numerical
1486derivative computation w/r to a GSAS-II variable. Keys are compiled
1487regular expressions and values are the step size for that parameter.
1488Initialized in :func:`CompileVarDesc`.
1489'''
1490# create a default space group object for P1; N.B. fails when building documentation
1491try:
1492    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1493except:
1494    pass
1495
1496def GetPhaseNames(fl):
1497    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1498    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1499
1500    :param file fl: opened .gpx file
1501    :return: list of phase names
1502    '''
1503    PhaseNames = []
1504    while True:
1505        try:
1506            data = cPickle.load(fl)
1507        except EOFError:
1508            break
1509        datum = data[0]
1510        if 'Phases' == datum[0]:
1511            for datus in data[1:]:
1512                PhaseNames.append(datus[0])
1513    fl.seek(0)          #reposition file
1514    return PhaseNames
1515
1516def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1517    '''Create a new phase dict with default values for various parameters
1518
1519    :param str Name: Name for new Phase
1520
1521    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1522      defaults to data for P 1
1523
1524    :param list cell: unit cell parameter list; defaults to
1525      [1.0,1.0,1.0,90.,90,90.,1.]
1526
1527    '''
1528    if SGData is None: SGData = P1SGData
1529    if cell is None: cell=[1.0,1.0,1.0,90.,90.,90.,1.]
1530    phaseData = {
1531        'ranId':ran.randint(0,sys.maxsize),
1532        'General':{
1533            'Name':Name,
1534            'Type':'nuclear',
1535            'Modulated':False,
1536            'AtomPtrs':[3,1,7,9],
1537            'SGData':SGData,
1538            'Cell':[False,]+cell,
1539            'Pawley dmin':1.0,
1540            'Data plot type':'None',
1541            'SH Texture':{
1542                'Order':0,
1543                'Model':'cylindrical',
1544                'Sample omega':[False,0.0],
1545                'Sample chi':[False,0.0],
1546                'Sample phi':[False,0.0],
1547                'SH Coeff':[False,{}],
1548                'SHShow':False,
1549                'PFhkl':[0,0,1],
1550                'PFxyz':[0,0,1],
1551                'PlotType':'Pole figure',
1552                'Penalty':[['',],0.1,False,1.0]}},
1553        'Atoms':[],
1554        'Drawing':{},
1555        'Histograms':{},
1556        'Pawley ref':[],
1557        'RBModels':{},
1558        }
1559    if Super and Super.get('Use',False):
1560        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1561        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])[1]
1562        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1563
1564    return phaseData
1565
1566def ReadCIF(URLorFile):
1567    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1568    (from James Hester).
1569    The open routine gets confused with DOS names that begin with a letter and colon
1570    "C:\\dir\" so this routine will try to open the passed name as a file and if that
1571    fails, try it as a URL
1572
1573    :param str URLorFile: string containing a URL or a file name. Code will try first
1574      to open it as a file and then as a URL.
1575
1576    :returns: a PyCifRW CIF object.
1577    '''
1578    import CifFile as cif # PyCifRW from James Hester
1579
1580    # alternate approach:
1581    #import urllib
1582    #ciffile = 'file:'+urllib.pathname2url(filename)
1583
1584    try:
1585        fp = open(URLorFile,'r')
1586        cf = cif.ReadCif(fp)
1587        fp.close()
1588        return cf
1589    except IOError:
1590        return cif.ReadCif(URLorFile)
1591
1592def TestIndexAll():
1593    '''Test if :func:`IndexAllIds` has been called to index all phases and
1594    histograms (this is needed before :func:`G2VarObj` can be used.
1595
1596    :returns: Returns True if indexing is needed.
1597    '''
1598    if PhaseIdLookup or AtomIdLookup or HistIdLookup:
1599        return False
1600    return True
1601       
1602def IndexAllIds(Histograms,Phases):
1603    '''Scan through the used phases & histograms and create an index
1604    to the random numbers of phases, histograms and atoms. While doing this,
1605    confirm that assigned random numbers are unique -- just in case lightning
1606    strikes twice in the same place.
1607
1608    Note: this code assumes that the atom random Id (ranId) is the last
1609    element each atom record.
1610
1611    This is called when phases & histograms are looked up
1612    in these places (only):
1613       
1614     * :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` (which loads the histograms and phases from a GPX file),
1615     * :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree` (which does the same thing but from the data tree.)
1616     * :meth:`~GSASIIdataGUI.GSASII.OnFileClose` (clears out an old project)
1617   
1618    Note that globals :data:`PhaseIdLookup` and :data:`PhaseRanIdLookup` are
1619    also set in :func:`AddPhase2Index` to temporarily assign a phase number
1620    as a phase is being imported.
1621 
1622    TODO: do we need a lookup for rigid body variables?
1623    '''
1624    # process phases and atoms
1625    PhaseIdLookup.clear()
1626    PhaseRanIdLookup.clear()
1627    AtomIdLookup.clear()
1628    AtomRanIdLookup.clear()
1629    ShortPhaseNames.clear()
1630    for ph in Phases:
1631        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1632        ranId = Phases[ph]['ranId']
1633        while ranId in PhaseRanIdLookup:
1634            # Found duplicate random Id! note and reassign
1635            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1636            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1637        pId = str(Phases[ph]['pId'])
1638        PhaseIdLookup[pId] = (ph,ranId)
1639        PhaseRanIdLookup[ranId] = pId
1640        shortname = ph  #[:10]
1641        while shortname in ShortPhaseNames.values():
1642            shortname = ph[:8] + ' ('+ pId + ')'
1643        ShortPhaseNames[pId] = shortname
1644        AtomIdLookup[pId] = {}
1645        AtomRanIdLookup[pId] = {}
1646        for iatm,at in enumerate(Phases[ph]['Atoms']):
1647            ranId = at[cia+8]
1648            while ranId in AtomRanIdLookup[pId]: # check for dups
1649                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1650                at[cia+8] = ranId = ran.randint(0,sys.maxsize)
1651            AtomRanIdLookup[pId][ranId] = str(iatm)
1652            if Phases[ph]['General']['Type'] == 'macromolecular':
1653                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1654            else:
1655                label = at[ct-1]
1656            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1657    # process histograms
1658    HistIdLookup.clear()
1659    HistRanIdLookup.clear()
1660    ShortHistNames.clear()
1661    for hist in Histograms:
1662        ranId = Histograms[hist]['ranId']
1663        while ranId in HistRanIdLookup:
1664            # Found duplicate random Id! note and reassign
1665            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1666            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1667        hId = str(Histograms[hist]['hId'])
1668        HistIdLookup[hId] = (hist,ranId)
1669        HistRanIdLookup[ranId] = hId
1670        shortname = hist[:15]
1671        while shortname in ShortHistNames.values():
1672            shortname = hist[:11] + ' ('+ hId + ')'
1673        ShortHistNames[hId] = shortname
1674
1675def AddPhase2Index(rdObj,filename):
1676    '''Add a phase to the index during reading
1677    Used where constraints are generated during import (ISODISTORT CIFs)       
1678    '''
1679    ranId = rdObj.Phase['ranId']
1680    ph = 'from  '+filename #  phase is not named yet
1681    if ranId in PhaseRanIdLookup: return
1682    maxph = -1
1683    for r in PhaseRanIdLookup:
1684        maxph = max(maxph,int(PhaseRanIdLookup[r]))
1685    PhaseRanIdLookup[ranId] = pId = str(maxph + 1)
1686    PhaseIdLookup[pId] = (ph,ranId)
1687    shortname = 'from '+ os.path.splitext((os.path.split(filename))[1])[0]
1688    while shortname in ShortPhaseNames.values():
1689        shortname = ph[:8] + ' ('+ pId + ')'
1690    ShortPhaseNames[pId] = shortname
1691    AtomIdLookup[pId] = {}
1692    AtomRanIdLookup[pId] = {}
1693    for iatm,at in enumerate(rdObj.Phase['Atoms']):
1694        ranId = at[-1]
1695        while ranId in AtomRanIdLookup[pId]: # check for dups
1696            print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1697            at[-1] = ranId = ran.randint(0,sys.maxsize)
1698        AtomRanIdLookup[pId][ranId] = str(iatm)
1699        #if Phases[ph]['General']['Type'] == 'macromolecular':
1700        #    label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1701        #else:
1702        #    label = at[ct-1]
1703        label = at[0]
1704        AtomIdLookup[pId][str(iatm)] = (label,ranId)
1705
1706def LookupAtomId(pId,ranId):
1707    '''Get the atom number from a phase and atom random Id
1708
1709    :param int/str pId: the sequential number of the phase
1710    :param int ranId: the random Id assigned to an atom
1711
1712    :returns: the index number of the atom (str)
1713    '''
1714    if not AtomRanIdLookup:
1715        raise Exception('Error: LookupAtomId called before IndexAllIds was run')
1716    if pId is None or pId == '':
1717        raise KeyError('Error: phase is invalid (None or blank)')
1718    pId = str(pId)
1719    if pId not in AtomRanIdLookup:
1720        raise KeyError('Error: LookupAtomId does not have phase '+pId)
1721    if ranId not in AtomRanIdLookup[pId]:
1722        raise KeyError('Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']')
1723    return AtomRanIdLookup[pId][ranId]
1724
1725def LookupAtomLabel(pId,index):
1726    '''Get the atom label from a phase and atom index number
1727
1728    :param int/str pId: the sequential number of the phase
1729    :param int index: the index of the atom in the list of atoms
1730
1731    :returns: the label for the atom (str) and the random Id of the atom (int)
1732    '''
1733    if not AtomIdLookup:
1734        raise Exception('Error: LookupAtomLabel called before IndexAllIds was run')
1735    if pId is None or pId == '':
1736        raise KeyError('Error: phase is invalid (None or blank)')
1737    pId = str(pId)
1738    if pId not in AtomIdLookup:
1739        raise KeyError('Error: LookupAtomLabel does not have phase '+pId)
1740    if index not in AtomIdLookup[pId]:
1741        raise KeyError('Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']')
1742    return AtomIdLookup[pId][index]
1743
1744def LookupPhaseId(ranId):
1745    '''Get the phase number and name from a phase random Id
1746
1747    :param int ranId: the random Id assigned to a phase
1748    :returns: the sequential Id (pId) number for the phase (str)
1749    '''
1750    if not PhaseRanIdLookup:
1751        raise Exception('Error: LookupPhaseId called before IndexAllIds was run')
1752    if ranId not in PhaseRanIdLookup:
1753        raise KeyError('Error: LookupPhaseId does not have ranId '+str(ranId))
1754    return PhaseRanIdLookup[ranId]
1755
1756def LookupPhaseName(pId):
1757    '''Get the phase number and name from a phase Id
1758
1759    :param int/str pId: the sequential assigned to a phase
1760    :returns:  (phase,ranId) where phase is the name of the phase (str)
1761      and ranId is the random # id for the phase (int)
1762    '''
1763    if not PhaseIdLookup:
1764        raise Exception('Error: LookupPhaseName called before IndexAllIds was run')
1765    if pId is None or pId == '':
1766        raise KeyError('Error: phase is invalid (None or blank)')
1767    pId = str(pId)
1768    if pId not in PhaseIdLookup:
1769        raise KeyError('Error: LookupPhaseName does not have index '+pId)
1770    return PhaseIdLookup[pId]
1771
1772def LookupHistId(ranId):
1773    '''Get the histogram number and name from a histogram random Id
1774
1775    :param int ranId: the random Id assigned to a histogram
1776    :returns: the sequential Id (hId) number for the histogram (str)
1777    '''
1778    if not HistRanIdLookup:
1779        raise Exception('Error: LookupHistId called before IndexAllIds was run')
1780    if ranId not in HistRanIdLookup:
1781        raise KeyError('Error: LookupHistId does not have ranId '+str(ranId))
1782    return HistRanIdLookup[ranId]
1783
1784def LookupHistName(hId):
1785    '''Get the histogram number and name from a histogram Id
1786
1787    :param int/str hId: the sequential assigned to a histogram
1788    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1789      and ranId is the random # id for the histogram (int)
1790    '''
1791    if not HistIdLookup:
1792        raise Exception('Error: LookupHistName called before IndexAllIds was run')
1793    if hId is None or hId == '':
1794        raise KeyError('Error: histogram is invalid (None or blank)')
1795    hId = str(hId)
1796    if hId not in HistIdLookup:
1797        raise KeyError('Error: LookupHistName does not have index '+hId)
1798    return HistIdLookup[hId]
1799
1800def fmtVarDescr(varname):
1801    '''Return a string with a more complete description for a GSAS-II variable
1802
1803    :param str varname: A full G2 variable name with 2 or 3 or 4
1804       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1805
1806    :returns: a string with the description
1807    '''
1808    s,l = VarDescr(varname)
1809    return s+": "+l
1810
1811def VarDescr(varname):
1812    '''Return two strings with a more complete description for a GSAS-II variable
1813
1814    :param str name: A full G2 variable name with 2 or 3 or 4
1815       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1816
1817    :returns: (loc,meaning) where loc describes what item the variable is mapped
1818      (phase, histogram, etc.) and meaning describes what the variable does.
1819    '''
1820
1821    # special handling for parameter names without a colon
1822    # for now, assume self-defining
1823    if varname.find(':') == -1:
1824        return "Global",varname
1825
1826    l = getVarDescr(varname)
1827    if not l:
1828        return ("invalid variable name ("+str(varname)+")!"),""
1829#        return "invalid variable name!",""
1830
1831    if not l[-1]:
1832        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1833
1834    if len(l) == 3:         #SASD variable name!
1835        s = 'component:'+l[1]
1836        return s,l[-1]
1837    s = ""
1838    if l[0] is not None and l[1] is not None: # HAP: keep short
1839        if l[2] == "Scale": # fix up ambigous name
1840            l[5] = "Phase fraction"
1841        if l[0] == '*':
1842            lbl = 'Seq. ref.'
1843        else:
1844            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1845        if l[1] == '*':
1846            hlbl = 'Seq. ref.'
1847        else:
1848            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1849        if hlbl[:4] == 'HKLF':
1850            hlbl = 'Xtl='+hlbl[5:]
1851        elif hlbl[:4] == 'PWDR':
1852            hlbl = 'Pwd='+hlbl[5:]
1853        else:
1854            hlbl = 'Hist='+hlbl
1855        s = "Ph="+str(lbl)+" * "+str(hlbl)
1856    else:
1857        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1858            l[5] = "Scale factor"
1859        if l[2] == 'Back': # background parameters are "special", alas
1860            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1861            l[-1] += ' #'+str(l[3])
1862        elif l[4] is not None: # rigid body parameter or modulation parm
1863            lbl = ShortPhaseNames.get(l[0],'phase?')
1864            if 'RB' in l[2]:    #rigid body parm
1865                s = "RB body #"+str(l[3])+" (type "+str(l[4])+") in "+str(lbl) + ','
1866            else: #modulation parm
1867                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1868        elif l[3] is not None: # atom parameter,
1869            lbl = ShortPhaseNames.get(l[0],'phase?')
1870            try:
1871                albl = LookupAtomLabel(l[0],l[3])[0]
1872            except KeyError:
1873                albl = 'Atom?'
1874            s = "Atom "+str(albl)+" in "+str(lbl)
1875        elif l[0] == '*':
1876            s = "All phases "
1877        elif l[0] is not None:
1878            lbl = ShortPhaseNames.get(l[0],'phase?')
1879            s = "Phase "+str(lbl)
1880        elif l[1] == '*':
1881            s = 'All hists'
1882        elif l[1] is not None:
1883            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1884            if hlbl[:4] == 'HKLF':
1885                hlbl = 'Xtl='+hlbl[5:]
1886            elif hlbl[:4] == 'PWDR':
1887                hlbl = 'Pwd='+hlbl[5:]
1888            else:
1889                hlbl = 'Hist='+hlbl
1890            s = str(hlbl)
1891    if not s:
1892        s = 'Global'
1893    return s,l[-1]
1894
1895def getVarDescr(varname):
1896    '''Return a short description for a GSAS-II variable
1897
1898    :param str name: A full G2 variable name with 2 or 3 or 4
1899       colons (<p>:<h>:name[:<a1>][:<a2>])
1900
1901    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1902      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1903      the histogram number and the atom number; `name` will always be
1904      a str; and `description` is str or `None`.
1905      If the variable name is incorrectly formed (for example, wrong
1906      number of colons), `None` is returned instead of a list.
1907    '''
1908    l = varname.split(':')
1909    if len(l) == 2:     #SASD parameter name
1910        return varname,l[0],getDescr(l[1])
1911    if len(l) == 3:
1912        l += [None,None]
1913    elif len(l) == 4:
1914        l += [None]
1915    elif len(l) != 5:
1916        return None
1917    for i in (0,1,3,4):
1918        if l[i] == "":
1919            l[i] = None
1920    l += [getDescr(l[2])]
1921    return l
1922
1923def CompileVarDesc():
1924    '''Set the values in the variable lookup tables
1925    (:attr:`reVarDesc` and :attr:`reVarStep`).
1926    This is called in :func:`getDescr` and :func:`getVarStep` so this
1927    initialization is always done before use.
1928
1929    Note that keys may contain regular expressions, where '[xyz]'
1930    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range
1931    of values). '.*' matches any string. For example::
1932
1933    'AUiso':'Atomic isotropic displacement parameter',
1934
1935    will match variable ``'p::AUiso:a'``.
1936    If parentheses are used in the key, the contents of those parentheses can be
1937    used in the value, such as::
1938
1939    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1940
1941    will match ``AU11``, ``AU23``,... and `U11`, `U23` etc will be displayed
1942    in the value when used.
1943
1944    '''
1945    if reVarDesc: return # already done
1946    for key,value in {
1947        # derived or other sequential vars
1948        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1949        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1950        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1951        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1952        # ambiguous, alas:
1953        'Scale' : 'Phase or Histogram scale factor',
1954        # Phase vars (p::<var>)
1955        'A([0-5])' : ('Reciprocal metric tensor component \\1',1e-5),
1956        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1957        # Atom vars (p::<var>:a)
1958        'dA([xyz])$' : ('change to atomic coordinate, \\1',1e-6),
1959        'A([xyz])$' : '\\1 fractional atomic coordinate',
1960        'AUiso':('Atomic isotropic displacement parameter',1e-4),
1961        'AU([123][123])':('Atomic anisotropic displacement parameter U\\1',1e-4),
1962        'Afrac': ('Atomic site fraction parameter',1e-5),
1963        'Amul': 'Atomic site multiplicity value',
1964        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1965        # Hist (:h:<var>) & Phase (HAP) vars (p:h:<var>)
1966        'Back': 'Background term',
1967        'BkPkint;(.*)':'Background peak #\\1 intensity',
1968        'BkPkpos;(.*)':'Background peak #\\1 position',
1969        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1970        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1971#        'Back File' : 'Background file name',
1972        'BF mult' : 'Background file multiplier',
1973        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1974        'D([123][123])' : 'Anisotropic strain coef. \\1',
1975        'Extinction' : 'Extinction coef.',
1976        'MD' : 'March-Dollase coef.',
1977        'Mustrain;.*' : 'Microstrain coef.',
1978        'Size;.*' : 'Crystallite size value',
1979        'eA$' : 'Cubic mustrain value',
1980        'Ep$' : 'Primary extinction',
1981        'Es$' : 'Secondary type II extinction',
1982        'Eg$' : 'Secondary type I extinction',
1983        'Flack' : 'Flack parameter',
1984        'TwinFr' : 'Twin fraction',
1985        'Layer Disp'  : 'Layer displacement along beam',
1986        #Histogram vars (:h:<var>)
1987        'Absorption' : 'Absorption coef.',
1988        'LayerDisp'  : 'Bragg-Brentano Layer displacement',
1989        'Displace([XY])' : ('Debye-Scherrer sample displacement \\1',0.1),
1990        'Lam' : ('Wavelength',1e-6),
1991        'I\\(L2\\)\\/I\\(L1\\)' : ('Ka2/Ka1 intensity ratio',0.001),
1992        'Polariz\\.' : ('Polarization correction',1e-3),
1993        'SH/L' : ('FCJ peak asymmetry correction',1e-4),
1994        '([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),
1995        '([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),
1996        'Zero' : 'Debye-Scherrer zero correction',
1997        'Shift' : 'Bragg-Brentano sample displ.',
1998        'SurfRoughA' : 'Bragg-Brenano surface roughness A',
1999        'SurfRoughB' : 'Bragg-Brenano surface roughness B',
2000        'Transparency' : 'Bragg-Brentano sample tranparency',
2001        'DebyeA' : 'Debye model amplitude',
2002        'DebyeR' : 'Debye model radius',
2003        'DebyeU' : 'Debye model Uiso',
2004        'RBV.*' : 'Vector rigid body parameter',
2005        'RBVO([aijk])' : 'Vector rigid body orientation parameter \\1',
2006        'RBVP([xyz])' : 'Vector rigid body \\1 position parameter',
2007        'RBVf' : 'Vector rigid body site fraction',
2008        'RBV([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
2009        'RBVU' : 'Residue rigid body group Uiso param.',
2010        'RBRO([aijk])' : 'Residue rigid body orientation parameter \\1',
2011        'RBRP([xyz])' : 'Residue rigid body \\1 position parameter',
2012        'RBRTr;.*' : 'Residue rigid body torsion parameter',
2013        'RBRf' : 'Residue rigid body site fraction',
2014        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
2015        'RBRU' : 'Residue rigid body group Uiso param.',
2016        'constr([0-9]*)' : 'Generated degree of freedom from constraint',
2017        'nv-(.+)' : 'New variable assignment with name \\1',
2018        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
2019        'mV([0-2])$' : 'Modulation vector component \\1',
2020        'Fsin'  :   'Sin site fraction modulation',
2021        'Fcos'  :   'Cos site fraction modulation',
2022        'Fzero'  :   'Crenel function offset',      #may go away
2023        'Fwid'   :   'Crenel function width',
2024        'Tmin'   :   'ZigZag/Block min location',
2025        'Tmax'   :   'ZigZag/Block max location',
2026        '([XYZ])max': 'ZigZag/Block max value for \\1',
2027        '([XYZ])sin'  : 'Sin position wave for \\1',
2028        '([XYZ])cos'  : 'Cos position wave for \\1',
2029        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
2030        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
2031        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
2032        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
2033        # PDF peak parms (l:<var>;l = peak no.)
2034        'PDFpos'  : 'PDF peak position',
2035        'PDFmag'  : 'PDF peak magnitude',
2036        'PDFsig'  : 'PDF peak std. dev.',
2037        # SASD vars (l:<var>;l = component)
2038        'Aspect ratio' : 'Particle aspect ratio',
2039        'Length' : 'Cylinder length',
2040        'Diameter' : 'Cylinder/disk diameter',
2041        'Thickness' : 'Disk thickness',
2042        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
2043        'Dist' : 'Interparticle distance',
2044        'VolFr' : 'Dense scatterer volume fraction',
2045        'epis' : 'Sticky sphere epsilon',
2046        'Sticky' : 'Stickyness',
2047        'Depth' : 'Well depth',
2048        'Width' : 'Well width',
2049        'Volume' : 'Particle volume',
2050        'Radius' : 'Sphere/cylinder/disk radius',
2051        'Mean' : 'Particle mean radius',
2052        'StdDev' : 'Standard deviation in Mean',
2053        'G$': 'Guinier prefactor',
2054        'Rg$': 'Guinier radius of gyration',
2055        'B$': 'Porod prefactor',
2056        'P$': 'Porod power',
2057        'Cutoff': 'Porod cutoff',
2058        'PkInt': 'Bragg peak intensity',
2059        'PkPos': 'Bragg peak position',
2060        'PkSig': 'Bragg peak sigma',
2061        'PkGam': 'Bragg peak gamma',
2062        'e([12][12])' : 'strain tensor e\\1',   # strain vars e11, e22, e12
2063        'Dcalc': 'Calc. d-spacing',
2064        'Back$': 'background parameter',
2065        'pos$': 'peak position',
2066        'int$': 'peak intensity',
2067        'WgtFrac':'phase weight fraction',
2068        'alpha':'TOF profile term',
2069        'alpha-[01]':'Pink profile term',
2070        'beta-[01q]':'TOF/Pink profile term',
2071        'sig-[012q]':'TOF profile term',
2072        'dif[ABC]':'TOF to d-space calibration',
2073        'C\\([0-9]*,[0-9]*\\)' : 'spherical harmonics preferred orientation coef.',
2074        'Pressure': 'Pressure level for measurement in MPa',
2075        'Temperature': 'T value for measurement, K',
2076        'FreePrm([123])': 'User defined measurement parameter \\1',
2077        'Gonio. radius': 'Distance from sample to detector, mm',
2078        }.items():
2079        # Needs documentation: HAP: LeBail, newLeBail
2080        # hist: Azimuth, Chi, Omega, Phi, Bank, nDebye, nPeaks
2081       
2082        if len(value) == 2:
2083            #VarDesc[key] = value[0]
2084            reVarDesc[re.compile(key)] = value[0]
2085            reVarStep[re.compile(key)] = value[1]
2086        else:
2087            #VarDesc[key] = value
2088            reVarDesc[re.compile(key)] = value
2089
2090def removeNonRefined(parmList):
2091    '''Remove items from variable list that are not refined and should not
2092    appear as options for constraints
2093
2094    :param list parmList: a list of strings of form "p:h:VAR:a" where
2095      VAR is the variable name
2096
2097    :returns: a list after removing variables where VAR matches a
2098      entry in local variable NonRefinedList
2099    '''
2100    NonRefinedList = ['Omega','Type','Chi','Phi', 'Azimuth','Gonio. radius',
2101                          'Lam1','Lam2','Back','Temperature','Pressure',
2102                          'FreePrm1','FreePrm2','FreePrm3',
2103                          'Source','nPeaks','LeBail','newLeBail','Bank',
2104                          'nDebye', #'',
2105                    ]
2106    return [prm for prm in parmList if prm.split(':')[2] not in NonRefinedList]
2107       
2108def getDescr(name):
2109    '''Return a short description for a GSAS-II variable
2110
2111    :param str name: The descriptive part of the variable name without colons (:)
2112
2113    :returns: a short description or None if not found
2114    '''
2115
2116    CompileVarDesc() # compile the regular expressions, if needed
2117    for key in reVarDesc:
2118        m = key.match(name)
2119        if m:
2120            reVarDesc[key]
2121            return m.expand(reVarDesc[key])
2122    return None
2123
2124def getVarStep(name,parmDict=None):
2125    '''Return a step size for computing the derivative of a GSAS-II variable
2126
2127    :param str name: A complete variable name (with colons, :)
2128    :param dict parmDict: A dict with parameter values or None (default)
2129
2130    :returns: a float that should be an appropriate step size, either from
2131      the value supplied in :func:`CompileVarDesc` or based on the value for
2132      name in parmDict, if supplied. If not found or the value is zero,
2133      a default value of 1e-5 is used. If parmDict is None (default) and
2134      no value is provided in :func:`CompileVarDesc`, then None is returned.
2135    '''
2136    CompileVarDesc() # compile the regular expressions, if needed
2137    for key in reVarStep:
2138        m = key.match(name)
2139        if m:
2140            return reVarStep[key]
2141    if parmDict is None: return None
2142    val = parmDict.get(key,0.0)
2143    if abs(val) > 0.05:
2144        return abs(val)/1000.
2145    else:
2146        return 1e-5
2147
2148def GenWildCard(varlist):
2149    '''Generate wildcard versions of G2 variables. These introduce '*'
2150    for a phase, histogram or atom number (but only for one of these
2151    fields) but only when there is more than one matching variable in the
2152    input variable list. So if the input is this::
2153
2154      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
2155
2156    then the output will be this::
2157
2158       wildList = ['*::AUiso:0', '0::AUiso:*']
2159
2160    :param list varlist: an input list of GSAS-II variable names
2161      (such as 0::AUiso:0)
2162
2163    :returns: wildList, the generated list of wild card variable names.
2164    '''
2165    wild = []
2166    for i in (0,1,3):
2167        currentL = varlist[:]
2168        while currentL:
2169            item1 = currentL.pop(0)
2170            i1splt = item1.split(':')
2171            if i >= len(i1splt): continue
2172            if i1splt[i]:
2173                nextL = []
2174                i1splt[i] = '[0-9]+'
2175                rexp = re.compile(':'.join(i1splt))
2176                matchlist = [item1]
2177                for nxtitem in currentL:
2178                    if rexp.match(nxtitem):
2179                        matchlist += [nxtitem]
2180                    else:
2181                        nextL.append(nxtitem)
2182                if len(matchlist) > 1:
2183                    i1splt[i] = '*'
2184                    wild.append(':'.join(i1splt))
2185                currentL = nextL
2186    return wild
2187
2188def LookupWildCard(varname,varlist):
2189    '''returns a list of variable names from list varname
2190    that match wildcard name in varname
2191
2192    :param str varname: a G2 variable name containing a wildcard
2193      (such as \\*::var)
2194    :param list varlist: the list of all variable names used in
2195      the current project
2196    :returns: a list of matching GSAS-II variables (may be empty)
2197    '''
2198    rexp = re.compile(varname.replace('*','[0-9]+'))
2199    return sorted([var for var in varlist if rexp.match(var)])
2200
2201def prmLookup(name,prmDict):
2202    '''Looks for a parameter in a min/max dictionary, optionally
2203    considering a wild card for histogram or atom number (use of
2204    both will never occur at the same time).
2205
2206    :param name: a GSAS-II parameter name (str, see :func:`getVarDescr`
2207      and :func:`CompileVarDesc`) or a :class:`G2VarObj` object.
2208    :param dict prmDict: a min/max dictionary, (parmMinDict
2209      or parmMaxDict in Controls) where keys are :class:`G2VarObj`
2210      objects.
2211    :returns: Two values, (**matchname**, **value**), are returned where:
2212
2213       * **matchname** *(str)* is the :class:`G2VarObj` object
2214         corresponding to the actual matched name,
2215         which could contain a wildcard even if **name** does not; and
2216       * **value** *(float)* which contains the parameter limit.
2217    '''
2218    for key,value in prmDict.items():
2219        if str(key) == str(name): return key,value
2220        if key == name: return key,value
2221    return None,None
2222       
2223
2224def _lookup(dic,key):
2225    '''Lookup a key in a dictionary, where None returns an empty string
2226    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
2227    '''
2228    if key is None:
2229        return ""
2230    elif key == "*":
2231        return "*"
2232    else:
2233        return dic.get(key,'?')
2234
2235def SortVariables(varlist):
2236    '''Sorts variable names in a sensible manner
2237    '''
2238    def cvnnums(var):
2239        v = []
2240        for i in var.split(':'):
2241#            if i == '' or i == '*':
2242#                v.append(-1)
2243#                continue
2244            try:
2245                v.append(int(i))
2246            except:
2247                v.append(-1)
2248        return v
2249    return sorted(varlist,key=cvnnums)
2250
2251class G2VarObj(object):
2252    '''Defines a GSAS-II variable either using the phase/atom/histogram
2253    unique Id numbers or using a character string that specifies
2254    variables by phase/atom/histogram number (which can change).
2255    Note that :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`,
2256    which calls :func:`IndexAllIds` (or
2257    :func:`GSASIIscriptable.G2Project.index_ids`) should be used to
2258    (re)load the current Ids
2259    before creating or later using the G2VarObj object.
2260
2261    This can store rigid body variables, but does not translate the residue # and
2262    body # to/from random Ids
2263
2264    A :class:`G2VarObj` object can be created with a single parameter:
2265
2266    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
2267      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
2268
2269     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
2270     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
2271     * a is the atom number (which may be left blank in which case the third colon is omitted).
2272       The atom number can be specified as '*' if a phase number is specified (not as '*').
2273       For rigid body variables, specify a will be a string of form "residue:body#"
2274
2275      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
2276      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
2277      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
2278      For a rigid body variables, AtomID is a string of form "residue:body#".
2279
2280    If four positional arguments are supplied, they are:
2281
2282    :param str/int phasenum: The number for the phase (or None or '*')
2283    :param str/int histnum: The number for the histogram (or None or '*')
2284    :param str varname: a single value can be used to create a :class:`G2VarObj`
2285    :param str/int atomnum: The number for the atom (or None or '*')
2286
2287    '''
2288    IDdict = {}
2289    IDdict['phases'] = {}
2290    IDdict['hists'] = {}
2291    IDdict['atoms'] = {}
2292    def __init__(self,*args):
2293        self.phase = None
2294        self.histogram = None
2295        self.name = ''
2296        self.atom = None
2297        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
2298            # single arg with 4 values
2299            self.phase,self.histogram,self.name,self.atom = args[0]
2300        elif len(args) == 1 and ':' in args[0]:
2301            #parse a string
2302            lst = args[0].split(':')
2303            if lst[0] == '*':
2304                self.phase = '*'
2305                if len(lst) > 3:
2306                    self.atom = lst[3]
2307                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2308            elif lst[1] == '*':
2309                self.histogram = '*'
2310                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2311            else:
2312                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2313                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2314                if len(lst) == 4:
2315                    if lst[3] == '*':
2316                        self.atom = '*'
2317                    else:
2318                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
2319                elif len(lst) == 5:
2320                    self.atom = lst[3]+":"+lst[4]
2321                elif len(lst) == 3:
2322                    pass
2323                else:
2324                    raise Exception("Incorrect number of colons in var name "+str(args[0]))
2325            self.name = lst[2]
2326        elif len(args) == 4:
2327            if args[0] == '*':
2328                self.phase = '*'
2329                self.atom = args[3]
2330            else:
2331                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
2332                if args[3] == '*':
2333                    self.atom = '*'
2334                elif args[0] is not None:
2335                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
2336            if args[1] == '*':
2337                self.histogram = '*'
2338            else:
2339                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
2340            self.name = args[2]
2341        else:
2342            raise Exception("Incorrectly called GSAS-II parameter name")
2343
2344        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
2345
2346    def __str__(self):
2347        return self.varname()
2348
2349    def __hash__(self):
2350        'Allow G2VarObj to be a dict key by implementing hashing'
2351        return hash(self.varname())
2352
2353    def varname(self,hist=None):
2354        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
2355        string (p:h:<var>:a) or (p:h:<var>)
2356
2357        :param str/int hist: if specified, overrides the histogram number
2358          with the specified value
2359        :returns: the variable name as a str
2360        '''
2361        a = ""
2362        if self.phase == "*":
2363            ph = "*"
2364            if self.atom:
2365                a = ":" + str(self.atom)
2366        else:
2367            ph = _lookup(PhaseRanIdLookup,self.phase)
2368            if self.atom == '*':
2369                a = ':*'
2370            elif self.atom:
2371                if ":" in str(self.atom):
2372                    a = ":" + str(self.atom)
2373                elif ph in AtomRanIdLookup:
2374                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
2375                else:
2376                    a = ":?"
2377        if hist is not None and self.histogram:
2378            hist = str(hist)
2379        elif self.histogram == "*":
2380            hist = "*"
2381        else:
2382            hist = _lookup(HistRanIdLookup,self.histogram)
2383        s = (ph + ":" + hist + ":" + str(self.name)) + a
2384        return s
2385
2386    def __repr__(self):
2387        '''Return the detailed contents of the object
2388        '''
2389        s = "<"
2390        if self.phase == '*':
2391            s += "Phases: all; "
2392            if self.atom is not None:
2393                if ":" in str(self.atom):
2394                    s += "Rigid body" + str(self.atom) + "; "
2395                else:
2396                    s += "Atom #" + str(self.atom) + "; "
2397        elif self.phase is not None:
2398            ph =  _lookup(PhaseRanIdLookup,self.phase)
2399            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
2400            if self.atom == '*':
2401                s += "Atoms: all; "
2402            elif ":" in str(self.atom):
2403                s += "Rigid body" + str(self.atom) + "; "
2404            elif self.atom is not None:
2405                s += "Atom rId=" + str(self.atom)
2406                if ph in AtomRanIdLookup:
2407                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
2408                else:
2409                    s += " (#? -- not found!); "
2410        if self.histogram == '*':
2411            s += "Histograms: all; "
2412        elif self.histogram is not None:
2413            hist = _lookup(HistRanIdLookup,self.histogram)
2414            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
2415        s += 'Variable name="' + str(self.name) + '">'
2416        return s+" ("+self.varname()+")"
2417
2418    def __eq__(self, other):
2419        '''Allow comparison of G2VarObj to other G2VarObj objects or strings.
2420        If any field is a wildcard ('*') that field matches.
2421        '''
2422        if type(other) is str:
2423            other = G2VarObj(other)
2424        elif type(other) is not G2VarObj:
2425            raise Exception("Invalid type ({}) for G2VarObj comparison with {}"
2426                            .format(type(other),other))
2427        if self.phase != other.phase and self.phase != '*' and other.phase != '*':
2428            return False
2429        if self.histogram != other.histogram and self.histogram != '*' and other.histogram != '*':
2430            return False
2431        if self.atom != other.atom and self.atom != '*' and other.atom != '*':
2432            return False
2433        if self.name != other.name:
2434            return False
2435        return True
2436   
2437    def fmtVarByMode(self, seqmode, note, warnmsg):
2438        '''Format a parameter object for display. Note that these changes
2439        are only temporary and are only shown only when the Constraints
2440        data tree is selected.
2441
2442        * In a non-sequential refinement or where the mode is 'use-all', the
2443          name is converted unchanged to a str
2444        * In a sequential refinement when the mode is 'wildcards-only' the
2445          name is converted unchanged to a str but a warning is added
2446          for non-wildcarded HAP or Histogram parameters
2447        * In a sequential refinement or where the mode is 'auto-wildcard',
2448          a histogram number is converted to a wildcard (*) and then
2449          converted to str
2450
2451        :param str mode: the sequential mode (see above)
2452        :param str note: value displayed on the line of the constraint/equiv.
2453        :param str warnmsg: a message saying the constraint is not used
2454
2455        :returns: varname, explain, note, warnmsg (all str values) where:
2456
2457          * varname is the parameter expressed as a string,
2458          * explain is blank unless there is a warning explanation about
2459            the parameter or blank
2460          * note is the previous value unless overridden
2461          * warnmsg is the previous value unless overridden
2462        '''
2463        explain = ''
2464        s = self.varname()
2465        if seqmode == 'auto-wildcard':
2466            if self.histogram: s = self.varname('*')
2467        elif seqmode == 'wildcards-only' and self.histogram:
2468            if self.histogram != '*':
2469                warnmsg = 'Ignored due to use of a non-wildcarded histogram number'
2470                note = 'Ignored'
2471                explain = '\nIgnoring: '+self.varname()+' does not contain a wildcard.\n'
2472        elif seqmode != 'use-all' and seqmode != 'wildcards-only':
2473            print('Unexpected mode',seqmode,' in fmtVarByMode')
2474        return s,explain,note,warnmsg
2475
2476    def _show(self):
2477        'For testing, shows the current lookup table'
2478        print ('phases'+ self.IDdict['phases'])
2479        print ('hists'+ self.IDdict['hists'])
2480        print ('atomDict'+ self.IDdict['atoms'])
2481
2482#==========================================================================
2483def SetDefaultSample():
2484    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
2485    return {
2486        'InstrName':'',
2487        'ranId':ran.randint(0,sys.maxsize),
2488        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
2489        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],
2490        'Temperature':300.,'Pressure':0.1,'Time':0.0,
2491        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
2492        'Gonio. radius':200.0,
2493        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
2494#SASD items
2495        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
2496        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
2497        'Trans':1.0,                            #measured transmission
2498        'SlitLen':0.0,                          #Slit length - in Q(A-1)
2499        }
2500######################################################################
2501class ImportBaseclass(object):
2502    '''Defines a base class for the reading of input files (diffraction
2503    data, coordinates,...). See :ref:`Writing a Import Routine<import_routines>`
2504    for an explanation on how to use a subclass of this class.
2505    '''
2506    class ImportException(Exception):
2507        '''Defines an Exception that is used when an import routine hits an expected error,
2508        usually in .Reader.
2509
2510        Good practice is that the Reader should define a value in self.errors that
2511        tells the user some information about what is wrong with their file.
2512        '''
2513        pass
2514
2515    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
2516    def __init__(self,formatName,longFormatName=None,
2517                 extensionlist=[],strictExtension=False,):
2518        self.formatName = formatName # short string naming file type
2519        if longFormatName: # longer string naming file type
2520            self.longFormatName = longFormatName
2521        else:
2522            self.longFormatName = formatName
2523        # define extensions that are allowed for the file type
2524        # for windows, remove any extensions that are duplicate, as case is ignored
2525        if sys.platform == 'windows' and extensionlist:
2526            extensionlist = list(set([s.lower() for s in extensionlist]))
2527        self.extensionlist = extensionlist
2528        # If strictExtension is True, the file will not be read, unless
2529        # the extension matches one in the extensionlist
2530        self.strictExtension = strictExtension
2531        self.errors = ''
2532        self.warnings = ''
2533        self.SciPy = False          #image reader needed scipy
2534        # used for readers that will use multiple passes to read
2535        # more than one data block
2536        self.repeat = False
2537        self.selections = []
2538        self.repeatcount = 0
2539        self.readfilename = '?'
2540        self.scriptable = False
2541        #print 'created',self.__class__
2542
2543    def ReInitialize(self):
2544        'Reinitialize the Reader to initial settings'
2545        self.errors = ''
2546        self.warnings = ''
2547        self.SciPy = False          #image reader needed scipy
2548        self.repeat = False
2549        self.repeatcount = 0
2550        self.readfilename = '?'
2551
2552
2553#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
2554#        '''This method must be supplied in the child class to read the file.
2555#        if the read fails either return False or raise an Exception
2556#        preferably of type ImportException.
2557#        '''
2558#        #start reading
2559#        raise ImportException("Error occurred while...")
2560#        self.errors += "Hint for user on why the error occur
2561#        return False # if an error occurs
2562#        return True # if read OK
2563
2564    def ExtensionValidator(self, filename):
2565        '''This methods checks if the file has the correct extension
2566       
2567        :returns:
2568       
2569          * False if this filename will not be supported by this reader (only
2570            when strictExtension is True)
2571          * True if the extension matches the list supplied by the reader
2572          * None if the reader allows un-registered extensions
2573         
2574        '''
2575        if filename:
2576            ext = os.path.splitext(filename)[1]
2577            if not ext and self.strictExtension: return False
2578            for ext in self.extensionlist:               
2579                if sys.platform == 'windows':
2580                    if filename.lower().endswith(ext): return True
2581                else:
2582                    if filename.endswith(ext): return True
2583        if self.strictExtension:
2584            return False
2585        else:
2586            return None
2587
2588    def ContentsValidator(self, filename):
2589        '''This routine will attempt to determine if the file can be read
2590        with the current format.
2591        This will typically be overridden with a method that
2592        takes a quick scan of [some of]
2593        the file contents to do a "sanity" check if the file
2594        appears to match the selected format.
2595        the file must be opened here with the correct format (binary/text)
2596        '''
2597        #filepointer.seek(0) # rewind the file pointer
2598        return True
2599
2600    def CIFValidator(self, filepointer):
2601        '''A :meth:`ContentsValidator` for use to validate CIF files.
2602        '''
2603        filepointer.seek(0)
2604        for i,l in enumerate(filepointer):
2605            if i >= 1000: return True
2606            '''Encountered only blank lines or comments in first 1000
2607            lines. This is unlikely, but assume it is CIF anyway, since we are
2608            even less likely to find a file with nothing but hashes and
2609            blank lines'''
2610            line = l.strip()
2611            if len(line) == 0: # ignore blank lines
2612                continue
2613            elif line.startswith('#'): # ignore comments
2614                continue
2615            elif line.startswith('data_'): # on the right track, accept this file
2616                return True
2617            else: # found something invalid
2618                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
2619                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
2620                    self.errors += '  '+str(l)
2621                else:
2622                    self.errors += '  (binary)'
2623                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
2624                self.errors += '\n        a data_ statement begins a block.'
2625                return False
2626
2627######################################################################
2628class ImportPhase(ImportBaseclass):
2629    '''Defines a base class for the reading of files with coordinates
2630
2631    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
2632    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` and in
2633    :func:`GSASIIscriptable.import_generic`.
2634    See :ref:`Writing a Import Routine<import_routines>`
2635    for an explanation on how to use this class.
2636
2637    '''
2638    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2639        strictExtension=False,):
2640        # call parent __init__
2641        ImportBaseclass.__init__(self,formatName,longFormatName,
2642            extensionlist,strictExtension)
2643        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
2644        self.SymOps = {} # specified when symmetry ops are in file (e.g. CIF)
2645        self.Constraints = None
2646
2647######################################################################
2648class ImportStructFactor(ImportBaseclass):
2649    '''Defines a base class for the reading of files with tables
2650    of structure factors.
2651
2652    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
2653    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
2654    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2655    :meth:`Reader`.
2656
2657    See :ref:`Writing a Import Routine<import_routines>`
2658    for an explanation on how to use import classes in general. The specifics
2659    for reading a structure factor histogram require that
2660    the ``Reader()`` routine in the import
2661    class need to do only a few things: It
2662    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2663    and set :attr:`Parameters` with the instrument parameters
2664    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2665    '''
2666    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2667        strictExtension=False,):
2668        ImportBaseclass.__init__(self,formatName,longFormatName,
2669            extensionlist,strictExtension)
2670
2671        # define contents of Structure Factor entry
2672        self.Parameters = []
2673        'self.Parameters is a list with two dicts for data parameter settings'
2674        self.InitParameters()
2675        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2676        self.Banks = []             #for multi bank data (usually TOF)
2677        '''self.RefDict is a dict containing the reflection information, as read from the file.
2678        Item 'RefList' contains the reflection information. See the
2679        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
2680        for the contents of each row. Dict element 'FF'
2681        contains the form factor values for each element type; if this entry
2682        is left as initialized (an empty list) it will be initialized as needed later.
2683        '''
2684    def ReInitialize(self):
2685        'Reinitialize the Reader to initial settings'
2686        ImportBaseclass.ReInitialize(self)
2687        self.InitParameters()
2688        self.Banks = []             #for multi bank data (usually TOF)
2689        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2690
2691    def InitParameters(self):
2692        'initialize the instrument parameters structure'
2693        Lambda = 0.70926
2694        HistType = 'SXC'
2695        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2696                            'Lam':[Lambda,Lambda]
2697                            }, {}]
2698        'Parameters is a list with two dicts for data parameter settings'
2699
2700    def UpdateParameters(self,Type=None,Wave=None):
2701        'Revise the instrument parameters'
2702        if Type is not None:
2703            self.Parameters[0]['Type'] = [Type,Type]
2704        if Wave is not None:
2705            self.Parameters[0]['Lam'] = [Wave,Wave]
2706
2707######################################################################
2708class ImportPowderData(ImportBaseclass):
2709    '''Defines a base class for the reading of files with powder data.
2710
2711    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2712    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder` and in
2713    :func:`GSASIIscriptable.import_generic`.
2714    See :ref:`Writing a Import Routine<import_routines>`
2715    for an explanation on how to use this class.
2716    '''
2717    def __init__(self,formatName,longFormatName=None,
2718        extensionlist=[],strictExtension=False,):
2719        ImportBaseclass.__init__(self,formatName,longFormatName,
2720            extensionlist,strictExtension)
2721        self.clockWd = None  # used in TOF
2722        self.ReInitialize()
2723
2724    def ReInitialize(self):
2725        'Reinitialize the Reader to initial settings'
2726        ImportBaseclass.ReInitialize(self)
2727        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2728        self.powderdata = [] # Powder dataset
2729        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2730                np.array(x), # x-axis values
2731                np.array(y), # powder pattern intensities
2732                np.array(w), # 1/sig(intensity)^2 values (weights)
2733                np.array(yc), # calc. intensities (zero)
2734                np.array(yb), # calc. background (zero)
2735                np.array(yd), # obs-calc profiles
2736        '''
2737        self.comments = []
2738        self.idstring = ''
2739        self.Sample = SetDefaultSample() # default sample parameters
2740        self.Controls = {}  # items to be placed in top-level Controls
2741        self.GSAS = None     # used in TOF
2742        self.repeat_instparm = True # Should a parm file be
2743        #                             used for multiple histograms?
2744        self.instparm = None # name hint from file of instparm to use
2745        self.instfile = '' # full path name to instrument parameter file
2746        self.instbank = '' # inst parm bank number
2747        self.instmsg = ''  # a label that gets printed to show
2748                           # where instrument parameters are from
2749        self.numbanks = 1
2750        self.instdict = {} # place items here that will be transferred to the instrument parameters
2751        self.pwdparms = {} # place parameters that are transferred directly to the tree
2752                           # here (typically from an existing GPX file)
2753######################################################################
2754class ImportSmallAngleData(ImportBaseclass):
2755    '''Defines a base class for the reading of files with small angle data.
2756    See :ref:`Writing a Import Routine<import_routines>`
2757    for an explanation on how to use this class.
2758    '''
2759    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2760        strictExtension=False,):
2761
2762        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2763            strictExtension)
2764        self.ReInitialize()
2765
2766    def ReInitialize(self):
2767        'Reinitialize the Reader to initial settings'
2768        ImportBaseclass.ReInitialize(self)
2769        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2770        self.smallangledata = [] # SASD dataset
2771        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2772                np.array(x), # x-axis values
2773                np.array(y), # powder pattern intensities
2774                np.array(w), # 1/sig(intensity)^2 values (weights)
2775                np.array(yc), # calc. intensities (zero)
2776                np.array(yd), # obs-calc profiles
2777                np.array(yb), # preset bkg
2778        '''
2779        self.comments = []
2780        self.idstring = ''
2781        self.Sample = SetDefaultSample()
2782        self.GSAS = None     # used in TOF
2783        self.clockWd = None  # used in TOF
2784        self.numbanks = 1
2785        self.instdict = {} # place items here that will be transferred to the instrument parameters
2786
2787######################################################################
2788class ImportReflectometryData(ImportBaseclass):
2789    '''Defines a base class for the reading of files with reflectometry data.
2790    See :ref:`Writing a Import Routine<import_routines>`
2791    for an explanation on how to use this class.
2792    '''
2793    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2794        strictExtension=False,):
2795
2796        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2797            strictExtension)
2798        self.ReInitialize()
2799
2800    def ReInitialize(self):
2801        'Reinitialize the Reader to initial settings'
2802        ImportBaseclass.ReInitialize(self)
2803        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2804        self.reflectometrydata = [] # SASD dataset
2805        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2806                np.array(x), # x-axis values
2807                np.array(y), # powder pattern intensities
2808                np.array(w), # 1/sig(intensity)^2 values (weights)
2809                np.array(yc), # calc. intensities (zero)
2810                np.array(yd), # obs-calc profiles
2811                np.array(yb), # preset bkg
2812        '''
2813        self.comments = []
2814        self.idstring = ''
2815        self.Sample = SetDefaultSample()
2816        self.GSAS = None     # used in TOF
2817        self.clockWd = None  # used in TOF
2818        self.numbanks = 1
2819        self.instdict = {} # place items here that will be transferred to the instrument parameters
2820
2821######################################################################
2822class ImportPDFData(ImportBaseclass):
2823    '''Defines a base class for the reading of files with PDF G(R) data.
2824    See :ref:`Writing a Import Routine<import_routines>`
2825    for an explanation on how to use this class.
2826    '''
2827    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2828        strictExtension=False,):
2829
2830        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2831            strictExtension)
2832        self.ReInitialize()
2833
2834    def ReInitialize(self):
2835        'Reinitialize the Reader to initial settings'
2836        ImportBaseclass.ReInitialize(self)
2837        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2838        self.pdfdata = [] # PDF G(R) dataset
2839        '''A pdf g(r) data set is a list with items [x,y]:
2840                np.array(x), # r-axis values
2841                np.array(y), # pdf g(r)
2842        '''
2843        self.comments = []
2844        self.idstring = ''
2845        self.numbanks = 1
2846
2847######################################################################
2848class ImportImage(ImportBaseclass):
2849    '''Defines a base class for the reading of images
2850
2851    Images are read in only these places:
2852
2853      * Initial reading is typically done from a menu item
2854        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2855        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2856        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2857        :meth:`Reader`. This returns a list of reader objects for each read image.
2858        Also used in :func:`GSASIIscriptable.import_generic`.
2859
2860      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2861        directly into the data tree.
2862
2863      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2864
2865    When reading an image, the ``Reader()`` routine in the ImportImage class
2866    should set:
2867
2868      * :attr:`Comments`: a list of strings (str),
2869      * :attr:`Npix`: the number of pixels in the image (int),
2870      * :attr:`Image`: the actual image as a numpy array (np.array)
2871      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2872        data items are needed:
2873
2874         * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2875         * 'wavelength': wavelength in :math:`\\AA`.
2876         * 'distance': distance of detector from sample in cm.
2877         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2878         * 'size': size of image (such as ``[2048,2048]``).
2879         * 'ImageTag': image number or other keyword used to retrieve image from
2880           a multi-image data file (defaults to ``1`` if not specified).
2881         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2882
2883    optional data items:
2884
2885      * :attr:`repeat`: set to True if there are additional images to
2886        read in the file, False otherwise
2887      * :attr:`repeatcount`: set to the number of the image.
2888
2889    Note that the above is initialized with :meth:`InitParameters`.
2890    (Also see :ref:`Writing a Import Routine<import_routines>`
2891    for an explanation on how to use import classes in general.)
2892    '''
2893    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2894        strictExtension=False,):
2895        ImportBaseclass.__init__(self,formatName,longFormatName,
2896            extensionlist,strictExtension)
2897        self.InitParameters()
2898
2899    def ReInitialize(self):
2900        'Reinitialize the Reader to initial settings -- not used at present'
2901        ImportBaseclass.ReInitialize(self)
2902        self.InitParameters()
2903
2904    def InitParameters(self):
2905        'initialize the instrument parameters structure'
2906        self.Comments = ['No comments']
2907        self.Data = {'samplechangerpos':0.0,'det2theta':0.0,'Gain map':''}
2908        self.Npix = 0
2909        self.Image = None
2910        self.repeat = False
2911        self.repeatcount = 1
2912        self.sumfile = ''
2913
2914    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2915        '''Optionally, call this after reading in an image to load it into the tree.
2916        This saves time by preventing a reread of the same information.
2917        '''
2918        if ParentFrame:
2919            ParentFrame.ImageZ = self.Image   # store the image for plotting
2920            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2921            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2922
2923#################################################################################################
2924# shortcut routines
2925exp = np.exp
2926sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2927cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2928tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2929sqrt = sq = lambda x: np.sqrt(x)
2930pi = lambda: np.pi
2931
2932def FindFunction(f):
2933    '''Find the object corresponding to function f
2934
2935    :param str f: a function name such as 'numpy.exp'
2936    :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2937      that defines the package location(s) and where pkgobj
2938      defines the object associated with the function.
2939      If the function is not found, pkgobj is None.
2940    '''
2941    df = f.split('.')
2942    pkgdict = {}
2943    # no listed module name, try in current namespace
2944    if len(df) == 1:
2945        try:
2946            fxnobj = eval(f)
2947            return pkgdict,fxnobj
2948        except (AttributeError, NameError):
2949            return None,None
2950
2951    # includes a package, see if package is already imported
2952    pkgnam = '.'.join(df[:-1])
2953    try:
2954        fxnobj = eval(f)
2955        pkgdict[pkgnam] = eval(pkgnam)
2956        return pkgdict,fxnobj
2957    except (AttributeError, NameError):
2958        pass
2959    # package not yet imported, so let's try
2960    if '.' not in sys.path: sys.path.append('.')
2961    pkgnam = '.'.join(df[:-1])
2962    #for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2963    #    if pkgname:
2964    #        pkgname += '.' + pkg
2965    #    else:
2966    #        pkgname = pkg
2967    try:
2968        exec('import '+pkgnam)
2969        pkgdict[pkgnam] = eval(pkgnam)
2970        fxnobj = eval(f)
2971    except Exception as msg:
2972        print('load of '+pkgnam+' failed with error='+str(msg))
2973        return {},None
2974    # can we access the function? I am not exactly sure what
2975    #    I intended this to test originally (BHT)
2976    try:
2977        fxnobj = eval(f,globals(),pkgdict)
2978        return pkgdict,fxnobj
2979    except Exception as msg:
2980        print('call to',f,' failed with error=',str(msg))
2981        return None,None # not found
2982               
2983class ExpressionObj(object):
2984    '''Defines an object with a user-defined expression, to be used for
2985    secondary fits or restraints. Object is created null, but is changed
2986    using :meth:`LoadExpression`. This contains only the minimum
2987    information that needs to be stored to save and load the expression
2988    and how it is mapped to GSAS-II variables.
2989    '''
2990    def __init__(self):
2991        self.expression = ''
2992        'The expression as a text string'
2993        self.assgnVars = {}
2994        '''A dict where keys are label names in the expression mapping to a GSAS-II
2995        variable. The value a G2 variable name.
2996        Note that the G2 variable name may contain a wild-card and correspond to
2997        multiple values.
2998        '''
2999        self.freeVars = {}
3000        '''A dict where keys are label names in the expression mapping to a free
3001        parameter. The value is a list with:
3002
3003         * a name assigned to the parameter
3004         * a value for to the parameter and
3005         * a flag to determine if the variable is refined.
3006        '''
3007        self.depVar = None
3008
3009        self.lastError = ('','')
3010        '''Shows last encountered error in processing expression
3011        (list of 1-3 str values)'''
3012
3013        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
3014        self.distance_atoms = None  # to be used for defining atom distances
3015
3016    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
3017        '''Load the expression and associated settings into the object. Raises
3018        an exception if the expression is not parsed, if not all functions
3019        are defined or if not all needed parameter labels in the expression
3020        are defined.
3021
3022        This will not test if the variable referenced in these definitions
3023        are actually in the parameter dictionary. This is checked when the
3024        computation for the expression is done in :meth:`SetupCalc`.
3025
3026        :param str expr: the expression
3027        :param list exprVarLst: parameter labels found in the expression
3028        :param dict varSelect: this will be 0 for Free parameters
3029          and non-zero for expression labels linked to G2 variables.
3030        :param dict varName: Defines a name (str) associated with each free parameter
3031        :param dict varValue: Defines a value (float) associated with each free parameter
3032        :param dict varRefflag: Defines a refinement flag (bool)
3033          associated with each free parameter
3034        '''
3035        self.expression = expr
3036        self.compiledExpr = None
3037        self.freeVars = {}
3038        self.assgnVars = {}
3039        for v in exprVarLst:
3040            if varSelect[v] == 0:
3041                self.freeVars[v] = [
3042                    varName.get(v),
3043                    varValue.get(v),
3044                    varRefflag.get(v),
3045                    ]
3046            else:
3047                self.assgnVars[v] = varName[v]
3048        self.CheckVars()
3049
3050    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
3051        '''Load the expression and associated settings from the object into
3052        arrays used for editing.
3053
3054        :param list exprVarLst: parameter labels found in the expression
3055        :param dict varSelect: this will be 0 for Free parameters
3056          and non-zero for expression labels linked to G2 variables.
3057        :param dict varName: Defines a name (str) associated with each free parameter
3058        :param dict varValue: Defines a value (float) associated with each free parameter
3059        :param dict varRefflag: Defines a refinement flag (bool)
3060          associated with each free parameter
3061
3062        :returns: the expression as a str
3063        '''
3064        for v in self.freeVars:
3065            varSelect[v] = 0
3066            varName[v] = self.freeVars[v][0]
3067            varValue[v] = self.freeVars[v][1]
3068            varRefflag[v] = self.freeVars[v][2]
3069        for v in self.assgnVars:
3070            varSelect[v] = 1
3071            varName[v] = self.assgnVars[v]
3072        return self.expression
3073
3074    def GetVaried(self):
3075        'Returns the names of the free parameters that will be refined'
3076        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
3077
3078    def GetVariedVarVal(self):
3079        'Returns the names and values of the free parameters that will be refined'
3080        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
3081
3082    def UpdateVariedVars(self,varyList,values):
3083        'Updates values for the free parameters (after a refinement); only updates refined vars'
3084        for v in self.freeVars:
3085            if not self.freeVars[v][2]: continue
3086            if "::"+self.freeVars[v][0] not in varyList: continue
3087            indx = list(varyList).index("::"+self.freeVars[v][0])
3088            self.freeVars[v][1] = values[indx]
3089
3090    def GetIndependentVars(self):
3091        'Returns the names of the required independent parameters used in expression'
3092        return [self.assgnVars[v] for v in self.assgnVars]
3093
3094    def CheckVars(self):
3095        '''Check that the expression can be parsed, all functions are
3096        defined and that input loaded into the object is internally
3097        consistent. If not an Exception is raised.
3098
3099        :returns: a dict with references to packages needed to
3100          find functions referenced in the expression.
3101        '''
3102        ret = self.ParseExpression(self.expression)
3103        if not ret:
3104            raise Exception("Expression parse error")
3105        exprLblList,fxnpkgdict = ret
3106        # check each var used in expression is defined
3107        defined = list(self.assgnVars.keys()) + list(self.freeVars.keys())
3108        notfound = []
3109        for var in exprLblList:
3110            if var not in defined:
3111                notfound.append(var)
3112        if notfound:
3113            msg = 'Not all variables defined'
3114            msg1 = 'The following variables were not defined: '
3115            msg2 = ''
3116            for var in notfound:
3117                if msg: msg += ', '
3118                msg += var
3119            self.lastError = (msg1,'  '+msg2)
3120            raise Exception(msg)
3121        return fxnpkgdict
3122
3123    def ParseExpression(self,expr):
3124        '''Parse an expression and return a dict of called functions and
3125        the variables used in the expression. Returns None in case an error
3126        is encountered. If packages are referenced in functions, they are loaded
3127        and the functions are looked up into the modules global
3128        workspace.
3129
3130        Note that no changes are made to the object other than
3131        saving an error message, so that this can be used for testing prior
3132        to the save.
3133
3134        :returns: a list of used variables
3135        '''
3136        self.lastError = ('','')
3137        import ast
3138        def ASTtransverse(node,fxn=False):
3139            '''Transverse a AST-parsed expresson, compiling a list of variables
3140            referenced in the expression. This routine is used recursively.
3141
3142            :returns: varlist,fxnlist where
3143              varlist is a list of referenced variable names and
3144              fxnlist is a list of used functions
3145            '''
3146            varlist = []
3147            fxnlist = []
3148            if isinstance(node, list):
3149                for b in node:
3150                    v,f = ASTtransverse(b,fxn)
3151                    varlist += v
3152                    fxnlist += f
3153            elif isinstance(node, ast.AST):
3154                for a, b in ast.iter_fields(node):
3155                    if isinstance(b, ast.AST):
3156                        if a == 'func':
3157                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
3158                            continue
3159                        v,f = ASTtransverse(b,fxn)
3160                        varlist += v
3161                        fxnlist += f
3162                    elif isinstance(b, list):
3163                        v,f = ASTtransverse(b,fxn)
3164                        varlist += v
3165                        fxnlist += f
3166                    elif node.__class__.__name__ == "Name":
3167                        varlist += [b]
3168                    elif fxn and node.__class__.__name__ == "Attribute":
3169                        varlist += [b]
3170            return varlist,fxnlist
3171        try:
3172            exprast = ast.parse(expr)
3173        except SyntaxError:
3174            s = ''
3175            import traceback
3176            for i in traceback.format_exc().splitlines()[-3:-1]:
3177                if s: s += "\n"
3178                s += str(i)
3179            self.lastError = ("Error parsing expression:",s)
3180            return
3181        # find the variables & functions
3182        v,f = ASTtransverse(exprast)
3183        varlist = sorted(list(set(v)))
3184        fxnlist = list(set(f))
3185        pkgdict = {}
3186        # check the functions are defined
3187        for fxn in fxnlist:
3188            fxndict,fxnobj = FindFunction(fxn)
3189            if not fxnobj:
3190                self.lastError = ("Error: Invalid function",fxn,
3191                                  "is not defined")
3192                return
3193            if not hasattr(fxnobj,'__call__'):
3194                self.lastError = ("Error: Not a function.",fxn,
3195                                  "cannot be called as a function")
3196                return
3197            pkgdict.update(fxndict)
3198        return varlist,pkgdict
3199
3200    def GetDepVar(self):
3201        'return the dependent variable, or None'
3202        return self.depVar
3203
3204    def SetDepVar(self,var):
3205        'Set the dependent variable, if used'
3206        self.depVar = var
3207#==========================================================================
3208class ExpressionCalcObj(object):
3209    '''An object used to evaluate an expression from a :class:`ExpressionObj`
3210    object.
3211
3212    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
3213      an expression string and mappings for the parameter labels in that object.
3214    '''
3215    def __init__(self,exprObj):
3216        self.eObj = exprObj
3217        'The expression and mappings; a :class:`ExpressionObj` object'
3218        self.compiledExpr = None
3219        'The expression as compiled byte-code'
3220        self.exprDict = {}
3221        '''dict that defines values for labels used in expression and packages
3222        referenced by functions
3223        '''
3224        self.lblLookup = {}
3225        '''Lookup table that specifies the expression label name that is
3226        tied to a particular GSAS-II parameters in the parmDict.
3227        '''
3228        self.fxnpkgdict = {}
3229        '''a dict with references to packages needed to
3230        find functions referenced in the expression.
3231        '''
3232        self.varLookup = {}
3233        '''Lookup table that specifies the GSAS-II variable(s)
3234        indexed by the expression label name. (Used for only for diagnostics
3235        not evaluation of expression.)
3236        '''
3237        self.su = None
3238        '''Standard error evaluation where supplied by the evaluator
3239        '''
3240        # Patch: for old-style expressions with a (now removed step size)
3241        if '2' in platform.python_version_tuple()[0]: 
3242            basestr = basestring
3243        else:
3244            basestr = str
3245        for v in self.eObj.assgnVars:
3246            if not isinstance(self.eObj.assgnVars[v], basestr):
3247                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
3248        self.parmDict = {}
3249        '''A copy of the parameter dictionary, for distance and angle computation
3250        '''
3251
3252    def SetupCalc(self,parmDict):
3253        '''Do all preparations to use the expression for computation.
3254        Adds the free parameter values to the parameter dict (parmDict).
3255        '''
3256        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3257            return
3258        self.fxnpkgdict = self.eObj.CheckVars()
3259        # all is OK, compile the expression
3260        self.compiledExpr = compile(self.eObj.expression,'','eval')
3261
3262        # look at first value in parmDict to determine its type
3263        parmsInList = True
3264        if '2' in platform.python_version_tuple()[0]: 
3265            basestr = basestring
3266        else:
3267            basestr = str
3268        for key in parmDict:
3269            val = parmDict[key]
3270            if isinstance(val, basestr):
3271                parmsInList = False
3272                break
3273            try: # check if values are in lists
3274                val = parmDict[key][0]
3275            except (TypeError,IndexError):
3276                parmsInList = False
3277            break
3278
3279        # set up the dicts needed to speed computations
3280        self.exprDict = {}
3281        self.lblLookup = {}
3282        self.varLookup = {}
3283        for v in self.eObj.freeVars:
3284            varname = self.eObj.freeVars[v][0]
3285            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
3286            self.lblLookup[varname] = v
3287            self.varLookup[v] = varname
3288            if parmsInList:
3289                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
3290            else:
3291                parmDict[varname] = self.eObj.freeVars[v][1]
3292            self.exprDict[v] = self.eObj.freeVars[v][1]
3293        for v in self.eObj.assgnVars:
3294            varname = self.eObj.assgnVars[v]
3295            if varname in parmDict:
3296                self.lblLookup[varname] = v
3297                self.varLookup[v] = varname
3298                if parmsInList:
3299                    self.exprDict[v] = parmDict[varname][0]
3300                else:
3301                    self.exprDict[v] = parmDict[varname]
3302            elif '*' in varname:
3303                varlist = LookupWildCard(varname,list(parmDict.keys()))
3304                if len(varlist) == 0:
3305                    raise Exception("No variables match "+str(v))
3306                for var in varlist:
3307                    self.lblLookup[var] = v
3308                if parmsInList:
3309                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
3310                else:
3311                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
3312                self.varLookup[v] = [var for var in varlist]
3313            else:
3314                self.exprDict[v] = None
3315#                raise Exception,"No value for variable "+str(v)
3316        self.exprDict.update(self.fxnpkgdict)
3317
3318    def UpdateVars(self,varList,valList):
3319        '''Update the dict for the expression with a set of values
3320        :param list varList: a list of variable names
3321        :param list valList: a list of corresponding values
3322        '''
3323        for var,val in zip(varList,valList):
3324            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
3325
3326    def UpdateDict(self,parmDict):
3327        '''Update the dict for the expression with values in a dict
3328        :param dict parmDict: a dict of values, items not in use are ignored
3329        '''
3330        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3331            self.parmDict = parmDict
3332            return
3333        for var in parmDict:
3334            if var in self.lblLookup:
3335                self.exprDict[self.lblLookup[var]] = parmDict[var]
3336
3337    def EvalExpression(self):
3338        '''Evaluate an expression. Note that the expression
3339        and mapping are taken from the :class:`ExpressionObj` expression object
3340        and the parameter values were specified in :meth:`SetupCalc`.
3341        :returns: a single value for the expression. If parameter
3342        values are arrays (for example, from wild-carded variable names),
3343        the sum of the resulting expression is returned.
3344
3345        For example, if the expression is ``'A*B'``,
3346        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
3347
3348        [0.5, 1, 0.5]
3349
3350        then the result will be ``4.0``.
3351        '''
3352        self.su = None
3353        if self.eObj.expression.startswith('Dist'):
3354#            GSASIIpath.IPyBreak()
3355            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
3356            return dist
3357        elif self.eObj.expression.startswith('Angle'):
3358            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
3359            return angle
3360        if self.compiledExpr is None:
3361            raise Exception("EvalExpression called before SetupCalc")
3362        try:
3363            val = eval(self.compiledExpr,globals(),self.exprDict)
3364        except TypeError:
3365            val = None
3366        if not np.isscalar(val):
3367            val = np.sum(val)
3368        return val
3369
3370class G2Exception(Exception):
3371    'A generic GSAS-II exception class'
3372    def __init__(self,msg):
3373        self.msg = msg
3374    def __str__(self):
3375        return repr(self.msg)
3376
3377class G2RefineCancel(Exception):
3378    'Raised when Cancel is pressed in a refinement dialog'
3379    def __init__(self,msg):
3380        self.msg = msg
3381    def __str__(self):
3382        return repr(self.msg)
3383   
3384def HowDidIgetHere(wherecalledonly=False):
3385    '''Show a traceback with calls that brought us to the current location.
3386    Used for debugging.
3387    '''
3388    import traceback
3389    if wherecalledonly:
3390        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
3391        print(i.strip().rstrip())
3392    else:
3393        print (70*'*')
3394        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
3395        print (70*'*')
3396
3397# Note that this is GUI code and should be moved at somepoint
3398def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
3399    '''Create and initialize a new set of PDF tree entries
3400
3401    :param Frame G2frame: main GSAS-II tree frame object
3402    :param str PWDRtree: name of PWDR to be used to create PDF item
3403    :param dict ElList: data structure with composition
3404    :param list Qlimits: Q limits to be used for computing the PDF
3405    :param float numAtm: no. atom in chemical formula
3406    :param float FltBkg: flat background value
3407    :param list PDFnames: previously used PDF names
3408
3409    :returns: the Id of the newly created PDF entry
3410    '''
3411    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
3412    if PDFname in PDFnames:
3413        print('Skipping, entry already exists: '+PDFname)
3414        return None
3415    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
3416    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
3417    Data = {
3418        'Sample':{'Name':PWDRtree,'Mult':1.0},
3419        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
3420        'Container':{'Name':'','Mult':-1.0,'Refine':False},
3421        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
3422        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
3423        'DetType':'Area detector','ObliqCoeff':0.3,'Ruland':0.025,'QScaleLim':Qlimits,
3424        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,'Rmin':1.0,
3425        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[],
3426        #items for sequential PDFfit
3427        'Datarange':[0.,30.],'Fitrange':[0.,30.],'qdamp':[0.03,False],'qbroad':[0,False],'Temp':300}
3428    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
3429    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
3430        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
3431    return Id
3432
3433class ShowTiming(object):
3434    '''An object to use for timing repeated sections of code.
3435
3436    Create the object with::
3437       tim0 = ShowTiming()
3438
3439    Tag sections of code to be timed with::
3440       tim0.start('start')
3441       tim0.start('in section 1')
3442       tim0.start('in section 2')
3443       
3444    etc. (Note that each section should have a unique label.)
3445
3446    After the last section, end timing with::
3447       tim0.end()
3448
3449    Show timing results with::
3450       tim0.show()
3451       
3452    '''
3453    def __init__(self):
3454        self.timeSum =  []
3455        self.timeStart = []
3456        self.label = []
3457        self.prev = None
3458    def start(self,label):
3459        import time
3460        if label in self.label:
3461            i = self.label.index(label)
3462            self.timeStart[i] = time.time()
3463        else:
3464            i = len(self.label)
3465            self.timeSum.append(0.0)
3466            self.timeStart.append(time.time())
3467            self.label.append(label)
3468        if self.prev is not None:
3469            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
3470        self.prev = i
3471    def end(self):
3472        import time
3473        if self.prev is not None:
3474            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
3475        self.prev = None
3476    def show(self):
3477        sumT = sum(self.timeSum)
3478        print('Timing results (total={:.2f} sec)'.format(sumT))
3479        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
3480            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
3481
3482def validateAtomDrawType(typ,generalData={}):
3483    '''Confirm that the selected Atom drawing type is valid for the current
3484    phase. If not, use 'vdW balls'. This is currently used only for setting a
3485    default when atoms are added to the atoms draw list.
3486    '''
3487    if typ in ('lines','vdW balls','sticks','balls & sticks','ellipsoids'):
3488        return typ
3489    # elif generalData.get('Type','') == 'macromolecular':
3490    #     if typ in ('backbone',):
3491    #         return typ
3492    return 'vdW balls'
3493
3494if __name__ == "__main__":
3495    # test variable descriptions
3496    for var in '0::Afrac:*',':1:Scale','1::dAx:0','::undefined':
3497        v = var.split(':')[2]
3498        print(var+':\t', getDescr(v),getVarStep(v))
3499    import sys; sys.exit()
3500    # test equation evaluation
3501    def showEQ(calcobj):
3502        print (50*'=')
3503        print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
3504        for v in sorted(calcobj.varLookup):
3505            print ("  "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
3506        # print '  Derivatives'
3507        # for v in calcobj.derivStep.keys():
3508        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
3509
3510    obj = ExpressionObj()
3511
3512    obj.expression = "A*np.exp(B)"
3513    obj.assgnVars =  {'B': '0::Afrac:1'}
3514    obj.freeVars =  {'A': [u'A', 0.5, True]}
3515    #obj.CheckVars()
3516    calcobj = ExpressionCalcObj(obj)
3517
3518    obj1 = ExpressionObj()
3519    obj1.expression = "A*np.exp(B)"
3520    obj1.assgnVars =  {'B': '0::Afrac:*'}
3521    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
3522    #obj.CheckVars()
3523    calcobj1 = ExpressionCalcObj(obj1)
3524
3525    obj2 = ExpressionObj()
3526    obj2.distance_stuff = np.array([[0,1],[1,-1]])
3527    obj2.expression = "Dist(1,2)"
3528    GSASIIpath.InvokeDebugOpts()
3529    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3530    calcobj2 = ExpressionCalcObj(obj2)
3531    calcobj2.SetupCalc(parmDict2)
3532    showEQ(calcobj2)
3533
3534    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
3535    print ('\nDict = '+parmDict1)
3536    calcobj.SetupCalc(parmDict1)
3537    showEQ(calcobj)
3538    calcobj1.SetupCalc(parmDict1)
3539    showEQ(calcobj1)
3540
3541    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3542    print ('Dict = '+parmDict2)
3543    calcobj.SetupCalc(parmDict2)
3544    showEQ(calcobj)
3545    calcobj1.SetupCalc(parmDict2)
3546    showEQ(calcobj1)
3547    calcobj2.SetupCalc(parmDict2)
3548    showEQ(calcobj2)
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