source: trunk/GSASIIobj.py @ 4823

Last change on this file since 4823 was 4823, checked in by toby, 9 months ago

fix naming of new variable constraints; label them & improve constraint help text

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Author Revision URL Id
File size: 163.4 KB
Line 
1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2021-02-20 19:25:23 +0000 (Sat, 20 Feb 2021) $
5# $Author: toby $
6# $Revision: 4823 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 4823 2021-02-20 19:25:23Z toby $
9########### SVN repository information ###################
10
11'''
12*GSASIIobj: Data objects*
13=========================
14
15This module defines and/or documents the data structures used in GSAS-II, as well
16as provides misc. support routines.
17
18.. Next command allows \\AA to be used in HTML
19
20.. only:: html
21
22   :math:`\\require{mediawiki-texvc}`
23
24.. _Constraints_table:
25
26.. index::
27   single: Constraints object description
28   single: Data object descriptions; Constraints
29
30Constraints Tree Item
31----------------------
32
33Constraints are stored in a dict, separated into groups.
34Note that parameter are named in the following pattern,
35p:h:<var>:n, where p is the phase number, h is the histogram number
36<var> is a variable name and n is the parameter number.
37If a parameter does not depend on a histogram or phase or is unnumbered, that
38number is omitted.
39Note that the contents of each dict item is a List where each element in the
40list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
41The constraints in this form are converted in
42:func:`GSASIIstrIO.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
43
44The keys in the Constraints dict are:
45
46.. tabularcolumns:: |l|p{4.5in}|
47
48==========  ====================================================
49  key         explanation
50==========  ====================================================
51Hist        This specifies a list of constraints on
52            histogram-related parameters,
53            which will be of form :h:<var>:n.
54HAP         This specifies a list of constraints on parameters
55            that are defined for every histogram in each phase
56            and are of form p:h:<var>:n.
57Phase       This specifies a list of constraints on phase
58            parameters,
59            which will be of form p::<var>:n.
60Global      This specifies a list of constraints on parameters
61            that are not tied to a histogram or phase and
62            are of form ::<var>:n
63==========  ====================================================
64
65.. _Constraint_definitions_table:
66
67.. index::
68   single: Constraint definition object description
69   single: Data object descriptions; Constraint Definition
70
71Each constraint is defined as an item in a list. Each constraint is of form::
72
73[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
74
75Where the variable pair list item containing two values [<mult>, <var>], where:
76
77  * <mult> is a multiplier for the constraint (float)
78  * <var> a :class:`G2VarObj` object (previously a str variable name of form
79      'p:h:name[:at]')
80
81Note that the last three items in the list play a special role:
82
83 * <fixedval> is the fixed value for a `constant equation` (``constype=c``)
84   constraint or is None. For a `New variable` (``constype=f``) constraint,
85   a variable name can be specified as a str (used for externally
86   generated constraints)
87 * <varyflag> is True or False for `New variable` (``constype=f``) constraints
88   or is None. This indicates if this variable should be refined.
89 * <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
90
91    * 'e' defines a set of equivalent variables. Only the first variable is refined (if the
92      appropriate refine flag is set) and and all other equivalent variables in the list
93      are generated from that variable, using the appropriate multipliers.
94    * 'c' defines a constraint equation of form,
95      :math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
96    * 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
97      even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
98      constraint and the mult value is ignored.
99      This is of particular value when needing to hold one or more variables where a
100      single flag controls a set of variables such as, coordinates,
101      the reciprocal metric tensor or anisotropic displacement parameter.
102    * 'f' defines a new variable (function) according to relationship
103      :math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
104
105.. _Covariance_table:
106
107.. index::
108   single: Covariance description
109   single: Data object descriptions; Covariance
110
111Covariance Tree Item
112--------------------
113
114The Covariance tree item has results from the last least-squares run. They
115are stored in a dict with these keys:
116
117.. tabularcolumns:: |l|l|p{4in}|
118
119=============  ===============  ====================================================
120  key            sub-key        explanation
121=============  ===============  ====================================================
122newCellDict    \\                (dict) ith lattice parameters computed by
123                                :func:`GSASIIstrMath.GetNewCellParms`
124title          \\                (str) Name of gpx file(?)
125variables      \\                (list) Values for all N refined variables
126                                (list of float values, length N,
127                                ordered to match varyList)
128sig            \\                (list) Uncertainty values for all N refined variables
129                                (list of float values, length N,
130                                ordered to match varyList)
131varyList       \\                (list of str values, length N) List of directly refined variables
132                               
133newAtomDict    \\                (dict) atom position values computed in
134                                :func:`GSASIIstrMath.ApplyXYZshifts`
135Rvals          \\                (dict) R-factors, GOF, Marquardt value for last
136                                refinement cycle
137\\              Nobs             (int) Number of observed data points
138\\              Rwp              (float) overall weighted profile R-factor (%)
139\\              chisq            (float) :math:`\\sum w*(I_{obs}-I_{calc})^2`                               
140                                for all data.
141                                Note: this is not the reduced :math:`\\chi^2`.
142\\              lamMax           (float) Marquardt value applied to Hessian diagonal
143\\              GOF              (float) The goodness-of-fit, aka square root of
144                                the reduced chi squared.
145covMatrix      \\                (np.array) The (NxN) covVariance matrix
146=============  ===============  ====================================================
147
148.. _Phase_table:
149
150.. index::
151   single: Phase object description
152   single: Data object descriptions; Phase
153
154Phase Tree Items
155----------------
156
157Phase information is stored in the GSAS-II data tree as children of the
158Phases item in a dict with keys:
159
160.. tabularcolumns:: |l|l|p{4in}|
161
162==========  ===============     =====================================================================================================
163  key         sub-key           explanation
164==========  ===============     =====================================================================================================
165General         \\               (dict) Overall information for the phase
166  \\         3Dproj              (list of str) projections for 3D pole distribution plots
167  \\         AngleRadii          (list of floats) Default radius for each atom used to compute
168                                interatomic angles
169  \\         AtomMass            (list of floats) Masses for atoms
170  \\         AtomPtrs            (list of int) four locations (cx,ct,cs & cu) to use to pull info
171                                from the atom records
172  \\         AtomTypes           (llist of str) Atom types
173  \\         BondRadii           (list of floats) Default radius for each atom used to compute
174                                interatomic distances
175  \\         Cell                Unit cell parameters & ref. flag
176                                (list with 8 items. All but first item are float.)
177
178                                 0: cell refinement flag (True/False),
179                                 1-3: a, b, c, (:math:`\\AA`)
180                                 4-6: alpha, beta & gamma, (degrees)
181                                 7: volume (:math:`\\AA^3`)
182  \\         Color               (list of (r,b,g) triplets) Colors for atoms
183  \\         Compare             (dict) Polygon comparison parameters
184  \\         Data plot type      (str) data plot type ('Mustrain', 'Size' or
185                                'Preferred orientation') for powder data
186  \\         DisAglCtls          (dDict) with distance/angle search controls,
187                                which has keys 'Name', 'AtomTypes',
188                                'BondRadii', 'AngleRadii' which are as above
189                                except are possibly edited. Also contains
190                                'Factors', which is a 2 element list with
191                                a multiplier for bond and angle search range
192                                [typically (0.85,0.85)].
193  \\         F000X               (float) x-ray F(000) intensity
194  \\         F000N               (float) neutron F(000) intensity
195  \\         Flip                (dict) Charge flip controls
196  \\         HydIds              (dict) geometrically generated hydrogen atoms
197  \\         Isotope             (dict) Isotopes for each atom type
198  \\         Isotopes            (dict) Scattering lengths for each isotope
199                                combination for each element in phase
200  \\         MCSA controls       (dict) Monte Carlo-Simulated Annealing controls
201  \\         Map                 (dict) Map parameters
202  \\         Mass                (float) Mass of unit cell contents in g/mol
203  \\         Modulated           (bool) True if phase modulated
204  \\         Mydir               (str) Directory of current .gpx file
205  \\         Name                (str) Phase name
206  \\         NoAtoms             (dict) Number of atoms per unit cell of each type
207  \\         POhkl               (list) March-Dollase preferred orientation direction
208  \\         Pawley dmin         (float) maximum Q (as d-space) to use for Pawley extraction
209  \\         Pawley dmax         (float) minimum Q (as d-space) to use for Pawley extraction
210  \\         Pawley neg wt       (float) Restraint value for negative Pawley intensities
211  \\         SGData              (object) Space group details as a
212                                :ref:`space group (SGData) <SGData_table>`
213                                object, as defined in :func:`GSASIIspc.SpcGroup`.
214  \\         SH Texture          (dict) Spherical harmonic preferred orientation parameters
215  \\         Super               (int) dimension of super group (0,1 only)
216  \\         Type                (str) phase type (e.g. 'nuclear')
217  \\         Z                   (dict) Atomic numbers for each atom type
218  \\         doDysnomia          (bool) flag for max ent map modification via Dysnomia
219  \\         doPawley            (bool) Flag for Pawley intensity extraction
220  \\         vdWRadii            (dict) Van der Waals radii for each atom type
221ranId           \\               (int) unique random number Id for phase
222pId             \\               (int) Phase Id number for current project.
223Atoms           \\               (list of lists) Atoms in phase as a list of lists. The outer list
224                                is for each atom, the inner list contains varying
225                                items depending on the type of phase, see
226                                the :ref:`Atom Records <Atoms_table>` description.
227Drawing         \\               (dict) Display parameters
228\\           Atoms               (list of lists) with an entry for each atom that is drawn
229\\           Plane               (list) Controls for contour density plane display
230\\           Quaternion          (4 element np.array) Viewing quaternion
231\\           Zclip               (float) clipping distance in :math:`\\AA`
232\\           Zstep               (float) Step to de/increase Z-clip
233\\           atomPtrs            (list) positions of x, type, site sym, ADP flag in Draw Atoms
234\\           backColor           (list) background for plot as and R,G,B triplet
235                                (default = [0, 0, 0], black).
236\\           ballScale           (float) Radius of spheres in ball-and-stick display
237\\           bondList            (dict) Bonds
238\\           bondRadius          (float) Radius of binds in :math:`\\AA`
239\\           cameraPos           (float) Viewing position in :math:`\\AA` for plot
240\\           contourLevel        (float) map contour level in :math:`e/\\AA^3`
241\\           contourMax          (float) map contour maximum
242\\           depthFog            (bool) True if use depthFog on plot - set currently as False
243\\           ellipseProb         (float) Probability limit for display of thermal
244                                ellipsoids in % .
245\\           magMult             (float) multiplier for magnetic moment arrows
246\\           mapSize             (float) x & y dimensions of contourmap (fixed internally)
247\\           modelView           (4,4 array) from openGL drawing transofmation matrix
248\\           oldxy               (list with two floats) previous view point
249\\           radiusFactor        (float) Distance ratio for searching for bonds. Bonds
250                                are located that are within r(Ra+Rb) and (Ra+Rb)/r
251                                where Ra and Rb are the atomic radii.
252\\           selectedAtoms       (list of int values) List of selected atoms
253\\           showABC             (bool) Flag to show view point triplet. True=show.
254\\           showHydrogen        (bool) Flag to control plotting of H atoms.
255\\           showRigidBodies     (bool) Flag to highlight rigid body placement
256\\           showSlice           (bool) flag to show contour map
257\\           sizeH               (float) Size ratio for H atoms
258\\           unitCellBox         (bool) Flag to control display of the unit cell.
259\\           vdwScale            (float) Multiplier of van der Waals radius for display of vdW spheres.
260\\           viewDir             (np.array with three floats) cartesian viewing direction
261\\           viewPoint           (list of lists) First item in list is [x,y,z]
262                                in fractional coordinates for the center of
263                                the plot. Second item list of previous & current
264                                atom number viewed (may be [0,0])
265RBModels        \\               Rigid body assignments (note Rigid body definitions
266                                are stored in their own main top-level tree entry.)
267RMC             \\               (dict) RMCProfile & rmcfull controls
268Pawley ref      \\               (list) Pawley reflections
269Histograms      \\               (dict of dicts) The key for the outer dict is
270                                the histograms tied to this phase. The inner
271                                dict contains the combined phase/histogram
272                                parameters for items such as scale factors,
273                                size and strain parameters. The following are the
274                                keys to the inner dict. (dict)
275\\           Babinet             (dict) For protein crystallography. Dictionary with two
276                                entries, 'BabA', 'BabU'
277\\           Extinction          (list of float, bool) Extinction parameter
278\\           Flack               (list of [float, bool]) Flack parameter & refine flag
279\\           HStrain             (list of two lists) Hydrostatic strain. The first is
280                                a list of the HStrain parameters (1, 2, 3, 4, or 6
281                                depending on unit cell), the second is a list of boolean
282                                refinement parameters (same length)
283\\           Histogram           (str) The name of the associated histogram
284\\           Layer Disp          (list of [float, bool]) Layer displacement in beam direction & refine flag
285\\           LeBail              (bool) Flag for LeBail extraction
286\\           Mustrain            (list) Microstrain parameters, in order:
287   
288                                0. Type, one of  u'isotropic', u'uniaxial', u'generalized'
289                                1. Isotropic/uniaxial parameters - list of 3 floats
290                                2. Refinement flags - list of 3 bools
291                                3. Microstrain axis - list of 3 ints, [h, k, l]
292                                4. Generalized mustrain parameters - list of 2-6 floats, depending on space group
293                                5. Generalized refinement flags - list of bools, corresponding to the parameters of (4)
294\\           Pref.Ori.           (list) Preferred Orientation. List of eight parameters.
295                                Items marked SH are only used for Spherical Harmonics.
296                               
297                                0. (str) Type, 'MD' for March-Dollase or 'SH' for Spherical Harmonics
298                                1. (float) Value
299                                2. (bool) Refinement flag
300                                3. (list) Preferred direction, list of ints, [h, k, l]
301                                4. (int) SH - number of terms
302                                5. (dict) SH - 
303                                6. (list) SH
304                                7. (float) SH
305\\           Scale               (list of [float, bool]) Phase fraction & refine flag
306\\           Size                List of crystallite size parameters, in order:
307
308                                0. (str) Type, one of  u'isotropic', u'uniaxial', u'ellipsoidal'
309                                1. (list) Isotropic/uniaxial parameters - list of 3 floats
310                                2. (list) Refinement flags - list of 3 bools
311                                3. (list) Size axis - list of 3 ints, [h, k, l]
312                                4. (list) Ellipsoidal size parameters - list of 6 floats
313                                5. (list) Ellipsoidal refinement flags - list of bools, corresponding to the parameters of (4)
314\\           Use                 (bool) True if this histogram is to be used in refinement
315\\           newLeBail           (bool) Whether to perform a new LeBail extraction
316MCSA            \\               (dict) Monte-Carlo simulated annealing parameters
317==========  ===============     =====================================================================================================
318
319.. _RBData_table:
320
321.. index::
322   single: Rigid Body Data description
323   single: Data object descriptions; Rigid Body Data
324
325Rigid Body Objects
326------------------
327
328Rigid body descriptions are available for two types of rigid bodies: 'Vector'
329and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
330with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
331with defined refinable torsion angles.
332
333.. tabularcolumns:: |l|l|p{4in}|
334
335==========  ===============     ====================================================
336  key         sub-key           explanation
337==========  ===============     ====================================================
338Vector      RBId                (dict of dict) vector rigid bodies
339\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
340\\           RBname              (str) Name assigned by user to rigid body
341\\           VectMag             (list) vector magnitudes in :math:`\\AA`
342\\           rbXYZ               (list of 3 float Cartesian coordinates for Vector rigid body )
343\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
344                                definition, use center of atoms flag
345\\           VectRef             (list of bool refinement flags for VectMag values )
346\\           rbTypes             (list of str) Atom types for each atom in rigid body
347\\           rbVect              (list of lists) Cartesian vectors for each translation used to build rigid body
348\\           useCount            (int) Number of times rigid body is used in any structure
349Residue     RBId                (dict of dict) residue rigid bodies
350\\           AtInfo              (dict) Drad, Color: atom drawing radius & color for each atom type
351\\           RBname              (str) Name assigned by user to rigid body
352\\           rbXYZ               (list of 3 float) Cartesian coordinates for Residue rigid body
353\\           rbTypes             (list of str) Atom types for each atom in rigid body
354\\           atNames             (list of str) Names of each atom in rigid body (e.g. C1,N2...)
355\\           rbRef               (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
356                                definition, use center of atoms flag
357\\           rbSeq               (list) Orig,Piv,angle,Riding : definition of internal rigid body
358                                torsion; origin atom (int), pivot atom (int), torsion angle (float),
359                                riding atoms (list of int)
360\\           SelSeq              (int,int) used by SeqSizer to identify objects
361\\           useCount            (int)Number of times rigid body is used in any structure
362RBIds           \\               (dict) unique Ids generated upon creation of each rigid body
363\\           Vector              (list) Ids for each Vector rigid body
364\\           Residue             (list) Ids for each Residue rigid body
365==========  ===============     ====================================================
366
367.. _SGData_table:
368
369.. index::
370   single: Space Group Data description
371   single: Data object descriptions; Space Group Data
372
373Space Group Objects
374-------------------
375
376Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
377and the information is placed in a SGdata object
378which is a dict with these keys. Magnetic ones are marked "mag"
379
380.. tabularcolumns:: |l|p{4.5in}|
381
382==========  ========================================================================================
383  key         explanation
384==========  ========================================================================================
385BNSlattsym  mag - (str) BNS magnetic space group symbol and centering vector
386GenFlg      mag - (list) symmetry generators indices
387GenSym      mag - (list) names for each generator
388MagMom      mag - (list) "time reversals" for each magnetic operator
389MagPtGp     mag - (str) Magnetic point group symbol
390MagSpGrp    mag - (str) Magnetic space group symbol
391OprNames    mag - (list) names for each space group operation
392SGCen       (np.array) Symmetry cell centering vectors. A (n,3) np.array
393            of centers. Will always have at least one row: ``np.array([[0, 0, 0]])``
394SGFixed     (bool) Only True if phase mported from a magnetic cif file
395            then the space group can not be changed by the user because
396            operator set from cif may be nonstandard
397SGGen       (list) generators
398SGGray      (bool) True if space group is a gray group (incommensurate magnetic structures)
399SGInv       (bool) True if centrosymmetric, False if not
400SGLatt      (str)Lattice centering type. Will be one of
401            P, A, B, C, I, F, R
402SGLaue      (str) one of the following 14 Laue classes:
403            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
404            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m
405SGOps       (list) symmetry operations as a list of form
406            ``[[M1,T1], [M2,T2],...]``
407            where :math:`M_n` is a 3x3 np.array
408            and :math:`T_n` is a length 3 np.array.
409            Atom coordinates are transformed where the
410            Asymmetric unit coordinates [X is (x,y,z)]
411            are transformed using
412            :math:`X^\\prime = M_n*X+T_n`
413SGPolax     (str) Axes for space group polarity. Will be one of
414            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
415            'xyz'. In the case where axes are arbitrary
416            '111' is used (P 1, and ?).
417SGPtGrp     (str) Point group of the space group
418SGUniq      unique axis if monoclinic. Will be
419            a, b, or c for monoclinic space groups.
420            Will be blank for non-monoclinic.
421SGSpin      mag - (list) of spin flip operatiors (+1 or -1) for the space group operations
422SGSys       (str) symmetry unit cell: type one of
423            'triclinic', 'monoclinic', 'orthorhombic',
424            'tetragonal', 'rhombohedral', 'trigonal',
425            'hexagonal', 'cubic'
426SSGK1       (list) Superspace multipliers
427SpGrp       (str) space group symbol
428SpnFlp      mag - (list) Magnetic spin flips for every magnetic space group operator
429==========  ========================================================================================
430
431.. _SSGData_table:
432
433.. index::
434   single: Superspace Group Data description
435   single: Data object descriptions; Superspace Group Data
436
437Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
438and the information is placed in a SSGdata object
439which is a dict with these keys:
440
441.. tabularcolumns:: |l|p{4.5in}|
442
443==========  ====================================================
444  key         explanation
445==========  ====================================================
446SSGCen      (list) 4D cell centering vectors [0,0,0,0] at least
447SSGK1       (list) Superspace multipliers
448SSGOps      (list) 4D symmetry operations as [M,T] so that M*x+T = x'
449SSpGrp      (str) superspace group symbol extension to space group
450            symbol, accidental spaces removed
451modQ        (list) modulation/propagation vector
452modSymb     (list of str) Modulation symbols
453==========  ====================================================
454
455
456Phase Information
457--------------------
458
459.. index::
460   single: Phase information record description
461
462Phase information is placed in one of the following keys:
463
464.. tabularcolumns:: |l|p{4.5in}|
465
466==========  ==============================================================
467  key         explanation
468==========  ==============================================================
469General       Overall information about a phase
470Histograms    Information about each histogram linked to the
471              current phase as well as parameters that
472              are defined for each histogram and phase
473              (such as sample peak widths and preferred
474              orientation parameters.
475Atoms         Contains a list of atoms, as described in the
476              :ref:`Atom Records <Atoms_table>` description.
477Drawing       Parameters that determine how the phase is
478              displayed, including a list of atoms to be
479              included, as described in the
480              :ref:`Drawing Atom Records <Drawing_atoms_table>`
481              description
482MCSA          Monte-Carlo simulated annealing parameters
483pId           The index of each phase in the project, numbered
484              starting at 0
485ranId         An int value with a unique value for each phase
486RBModels      A list of dicts with parameters for each
487              rigid body inserted into the current phase,
488              as defined in the
489              :ref:`Rigid Body Insertions <Rigid_Body_Insertions>`.
490              Note that the rigid bodies are defined as
491              :ref:`Rigid Body Objects <RBData_table>`
492RMC           PDF modeling parameters
493Pawley ref    Pawley refinement parameters
494
495==========  ==============================================================
496
497.. _Atoms_table:
498
499.. index::
500   single: Atoms record description
501   single: Data object descriptions; Atoms record
502
503--------------------
504Atom Records
505--------------------
506
507If ``phasedict`` points to the phase information in the data tree, then
508atoms are contained in a list of atom records (list) in
509``phasedict['Atoms']``. Also needed to read atom information
510are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
511which define locations in the atom record, as shown below. Items shown are
512always present; additional ones for macromolecular phases are marked 'mm',
513and those for magnetic structures are marked 'mg'
514
515.. tabularcolumns:: |l|p{4.5in}|
516
517==============      ====================================================
518location            explanation
519==============      ====================================================
520ct-4                mm - (str) residue number
521ct-3                mm - (str) residue name (e.g. ALA)
522ct-2                mm - (str) chain label
523ct-1                (str) atom label
524ct                  (str) atom type
525ct+1                (str) refinement flags; combination of 'F', 'X', 'U', 'M'
526cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
527cx+3                (float) site occupancy
528cx+4,cx+5,cx+6      mg - (list) atom magnetic moment along a,b,c in Bohr magnetons
529cs                  (str) site symmetry
530cs+1                (int) site multiplicity
531cia                 (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
532cia+1               (float) Uiso
533cia+2...cia+7       (6 floats) U11, U22, U33, U12, U13, U23
534atom[cia+8]         (int) unique atom identifier
535
536==============      ====================================================
537
538.. _Drawing_atoms_table:
539
540.. index::
541   single: Drawing atoms record description
542   single: Data object descriptions; Drawing atoms record
543
544----------------------------
545Drawing Atom Records
546----------------------------
547
548If ``phasedict`` points to the phase information in the data tree, then
549drawing atoms are contained in a list of drawing atom records (list) in
550``phasedict['Drawing']['Atoms']``. Also needed to read atom information
551are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
552which define locations in the atom record, as shown below. Items shown are
553always present; additional ones for macromolecular phases are marked 'mm',
554and those for magnetic structures are marked 'mg'
555
556.. tabularcolumns:: |l|p{4.5in}|
557
558==============   ===================================================================================
559location            explanation
560==============   ===================================================================================
561ct-4                mm - (str) residue number
562ct-3                mm - (str) residue name (e.g. ALA)
563ct-2                mm - (str) chain label
564ct-1                (str) atom label
565ct                  (str) atom type
566cx,cx+1,cx+2        (3 floats) the x,y and z coordinates
567cx+3,cx+4,cx+5      mg - (3 floats) atom magnetic moment along a,b,c in Bohr magnetons
568cs-1                (str) Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1')
569cs                  (str) atom drawing style; e.g. 'balls & sticks'
570cs+1                (str) atom label style (e.g. 'name')
571cs+2                (int) atom color (RBG triplet)
572cs+3                (str) ADP flag: Isotropic ('I') or Anisotropic ('A')
573cs+4                (float) Uiso
574cs+5...cs+11        (6 floats) U11, U22, U33, U12, U13, U23
575ci                  (int) unique atom identifier; matches source atom Id in Atom Records
576==============   ===================================================================================
577
578.. _Rigid_Body_Insertions:
579
580----------------------------
581Rigid Body Insertions
582----------------------------
583
584If ``phasedict`` points to the phase information in the data tree, then
585rigid body information is contained in list(s) in
586``phasedict['RBModels']['Residue']`` and/or ``phasedict['RBModels']['Vector']``
587for each rigid body inserted into the current phase.
588
589.. tabularcolumns:: |l|p{4.5in}|
590
591==============   ===================================================================================
592key              explanation
593==============   ===================================================================================
594fixOrig           Should the origin be fixed (when editing, not the refinement flag)
595Ids               Ids for assignment of atoms in the rigid body
596numChain          Chain number for macromolecular fits
597Orient            Orientation of the RB as a quaternion and a refinement flag (' ', 'A' or 'AV')
598OrientVec         Orientation of the RB expressed as a vector and azimuthal rotation angle
599Orig              Origin of the RB in fractional coordinates and refinement flag (bool)
600RBId              References the unique ID of a rigid body in the
601                  :ref:`Rigid Body Objects <RBData_table>`
602RBname            The name for the rigid body (str)
603ThermalMotion     The thermal motion description for the rigid body, which includes a choice for
604                  the model and can include TLS parameters or an overall Uiso value.
605Torsions          Defines the torsion angle and refinement flag for each torsion defined in
606                  the :ref:`Rigid Body Object <RBData_table>`
607==============   ===================================================================================
608
609.. _Powder_table:
610
611.. index::
612   single: Powder data object description
613   single: Data object descriptions; Powder Data
614
615Powder Diffraction Tree Items
616-----------------------------
617
618Every powder diffraction histogram is stored in the GSAS-II data tree
619with a top-level entry named beginning with the string "PWDR ". The
620diffraction data for that information are directly associated with
621that tree item and there are a series of children to that item. The
622routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
623and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
624load this information into a dictionary where the child tree name is
625used as a key, and the information in the main entry is assigned
626a key of ``Data``, as outlined below.
627
628.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
629
630======================     ===============  ===========================================================
631  key                       sub-key          explanation
632======================     ===============  ===========================================================
633Comments                    \\               (list of str) Text strings extracted from the original powder
634                                            data header. These cannot be changed by the user;
635                                            it may be empty.
636Limits                      \\               (list) two two element lists, as [[Ld,Hd],[L,H]]
637                                            where L and Ld are the current and default lowest
638                                            two-theta value to be used and
639                                            where H and Hd are the current and default highest
640                                            two-theta value to be used.
641Reflection Lists            \\               (dict of dicts) with an entry for each phase in the
642                                            histogram. The contents of each dict item
643                                            is a dict containing reflections, as described in
644                                            the :ref:`Powder Reflections <PowderRefl_table>`
645                                            description.
646Instrument Parameters       \\               (dict) The instrument parameters uses different dicts
647                                            for the constant wavelength (CW) and time-of-flight (TOF)
648                                            cases. See below for the descriptions of each.
649wtFactor                    \\               (float) A weighting factor to increase or decrease
650                                            the leverage of data in the histogram .
651                                            A value of 1.0 weights the data with their
652                                            standard uncertainties and a larger value
653                                            increases the weighting of the data (equivalent
654                                            to decreasing the uncertainties).
655Sample Parameters           \\               (dict) Parameters that describe how
656                                            the data were collected, as listed
657                                            below. Refinable parameters are a list containing
658                                            a float and a bool, where the second value
659                                            specifies if the value is refined, otherwise
660                                            the value is a float unless otherwise noted.
661\\                           Scale           The histogram scale factor (refinable)
662\\                           Absorption      The sample absorption coefficient as
663                                            :math:`\\mu r` where r is the radius
664                                            (refinable). Only valid for Debye-Scherrer geometry.
665\\                           SurfaceRoughA   Surface roughness parameter A as defined by
666                                            Surotti, *J. Appl. Cryst*, **5**, 325-331, 1972.
667                                            (refinable - only valid for Bragg-Brentano geometry)
668\\                           SurfaceRoughB   Surface roughness parameter B (refinable -
669                                            only valid for Bragg-Brentano geometry)
670\\                           DisplaceX,      Sample displacement from goniometer center
671                            DisplaceY       where Y is along the beam direction and
672                                            X is perpendicular. Units are :math:`\\mu m`
673                                            (refinable).
674\\                           Phi, Chi,       Goniometer sample setting angles, in degrees.
675                            Omega
676\\                           Gonio. radius   Radius of the diffractometer in mm
677\\                           InstrName       (str) A name for the instrument, used in preparing
678                                            a CIF .
679\\                           Force,          Variables that describe how the measurement
680                            Temperature,    was performed. Not used directly in
681                            Humidity,       any computations.
682                            Pressure,
683                            Voltage
684\\                           ranId           (int) The random-number Id for the histogram
685                                            (same value as where top-level key is ranId)
686\\                           Type            (str) Type of diffraction data, may be 'Debye-Scherrer'
687                                            or 'Bragg-Brentano' .
688hId                         \\               (int) The number assigned to the histogram when
689                                            the project is loaded or edited (can change)
690ranId                       \\               (int) A random number id for the histogram
691                                            that does not change
692Background                  \\               (list) The background is stored as a list with where
693                                            the first item in the list is list and the second
694                                            item is a dict. The list contains the background
695                                            function and its coefficients; the dict contains
696                                            Debye diffuse terms and background peaks.
697                                            (TODO: this needs to be expanded.)
698Data                        \\               (list) The data consist of a list of 6 np.arrays
699                                            containing in order:
700
701                                            0. the x-postions (two-theta in degrees),
702                                            1. the intensity values (Yobs),
703                                            2. the weights for each Yobs value
704                                            3. the computed intensity values (Ycalc)
705                                            4. the background values
706                                            5. Yobs-Ycalc
707======================     ===============  ===========================================================
708
709.. _CWPowder_table:
710
711.. index::
712   single: Powder data CW Instrument Parameters
713
714-----------------------------
715CW Instrument Parameters
716-----------------------------
717
718Instrument Parameters are placed in a list of two dicts,
719where the keys in the first dict are listed below. Note that the dict contents are different for
720constant wavelength (CW) vs. time-of-flight (TOF) histograms.
721The value for each item is a list containing three values: the initial value, the current value
722and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
723cannot be refined. The first and second values are floats unless otherwise noted.
724Items not refined are noted as [*]
725
726.. tabularcolumns:: |l|p{1in}|p{4in}|
727
728========================    ===============  ===========================================================
729  key                       sub-key           explanation
730========================    ===============  ===========================================================
731Instrument Parameters[0]    Type [*]            (str) Histogram type:
732                                                * 'PXC' for constant wavelength x-ray
733                                                * 'PNC' for constant wavelength neutron
734\\                           Bank [*]            (int) Data set number in a multidata file (usually 1)
735\\                           Lam                 (float) Specifies a wavelength in :math:`\\AA`
736\\                           Lam1 [*]            (float) Specifies the primary wavelength in
737                                                :math:`\\AA`, used in place of Lam
738                                                when an :math:`\\alpha_1, \\alpha_2`
739                                                source is used.
740\\                           Lam2 [*]            (float) Specifies the secondary wavelength in
741                                                :math:`\\AA`, used with Lam1
742\\                           I(L2)/I(L1)         (float) Ratio of Lam2 to Lam1, used with Lam1
743\\                           Zero                (float) Two-theta zero correction in *degrees*
744\\                           Azimuth [*]         (float) Azimuthal setting angle for data recorded with differing setting angles
745\\                           U, V, W             (float) Cagliotti profile coefficients
746                                                for Gaussian instrumental broadening, where the
747                                                FWHM goes as
748                                                :math:`U \\tan^2\\theta + V \\tan\\theta + W`
749\\                           X, Y, Z             (float) Cauchy (Lorentzian) instrumental broadening coefficients
750\\                           SH/L                (float) Variant of the Finger-Cox-Jephcoat asymmetric
751                                                peak broadening ratio. Note that this is the
752                                                sum of S/L and H/L where S is
753                                                sample height, H is the slit height and
754                                                L is the goniometer diameter.
755\\                           Polariz.            (float) Polarization coefficient.
756Instrument Parameters[1]                        (empty dict)
757========================    ===============  ===========================================================
758
759.. _TOFPowder_table:
760
761.. index::
762   single: Powder data TOF Instrument Parameters
763
764-----------------------------
765TOF Instrument Parameters
766-----------------------------
767
768Instrument Parameters are also placed in a list of two dicts,
769where the keys in each dict listed below, but here for
770time-of-flight (TOF) histograms.
771The value for each item is a list containing three values: the initial value, the current value
772and a refinement flag which can have a value of True, False or 0 where 0 indicates a value that
773cannot be refined. The first and second values are floats unless otherwise noted.
774Items not refined are noted as [*]
775
776.. tabularcolumns:: |l|p{1.5in}|p{4in}|
777
778========================    ===============  ===========================================================
779  key                        sub-key          explanation
780========================    ===============  ===========================================================
781Instrument Parameters[0]    Type [*]            (str) Histogram type:
782                                                * 'PNT' for time of flight neutron
783\\                           Bank                (int) Data set number in a multidata file
784\\                           2-theta [*]         (float) Nominal scattering angle for the detector
785\\                           fltPath [*]         (float) Total flight path source-sample-detector
786\\                           Azimuth [*]         (float) Azimuth angle for detector right hand rotation
787                                                from horizontal away from source
788\\                           difC,difA,          (float) Diffractometer constants for conversion of d-spacing to TOF
789                            difB                in microseconds
790\\                           Zero                (float) Zero point offset (microseconds)
791\\                           alpha               (float) Exponential rise profile coefficients
792\\                           beta-0              (float) Exponential decay profile coefficients
793                            beta-1
794                            beta-q
795\\                           sig-0               (float) Gaussian profile coefficients
796                            sig-1
797                            sig-2
798                            sig-q   
799\\                           X,Y,Z               (float) Lorentzian profile coefficients
800Instrument Parameters[1]    Pdabc               (list of 4 float lists) Originally created for use in gsas as optional tables
801                                                of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation
802                                                from the d-spacing and these tables. The d-true column is apparently unused.
803========================    ===============  ===========================================================
804
805
806.. _PowderRefl_table:
807
808.. index::
809   single: Powder reflection object description
810   single: Data object descriptions; Powder Reflections
811
812Powder Reflection Data Structure
813--------------------------------
814
815For every phase in a histogram, the ``Reflection Lists`` value is a dict
816one element of which is `'RefList'`, which is a np.array containing
817reflections. The columns in that array are documented below.
818
819==========  ====================================================
820  index         explanation
821==========  ====================================================
822 0,1,2          h,k,l (float)
823 3              (int) multiplicity
824 4              (float) d-space, :math:`\\AA`
825 5              (float) pos, two-theta
826 6              (float) sig, Gaussian width
827 7              (float) gam, Lorenzian width
828 8              (float) :math:`F_{obs}^2`
829 9              (float) :math:`F_{calc}^2`
830 10             (float) reflection phase, in degrees
831 11             (float) intensity correction for reflection, this times
832                :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
833 12             (float) Preferred orientation correction
834 13             (float) Transmission (absorption correction)
835 14             (float) Extinction correction
836==========  ====================================================
837
838.. _Xtal_table:
839
840.. index::
841   single: Single Crystal data object description
842   single: Data object descriptions; Single crystal data
843
844Single Crystal Tree Items
845-------------------------
846
847Every single crystal diffraction histogram is stored in the GSAS-II data tree
848with a top-level entry named beginning with the string "HKLF ". The
849diffraction data for that information are directly associated with
850that tree item and there are a series of children to that item. The
851routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
852and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
853load this information into a dictionary where the child tree name is
854used as a key, and the information in the main entry is assigned
855a key of ``Data``, as outlined below.
856
857.. tabularcolumns:: |l|l|p{4in}|
858
859======================  ===============     ====================================================
860  key                      sub-key          explanation
861======================  ===============     ====================================================
862Data                        \\               (dict) that contains the
863                                            reflection table,
864                                            as described in the
865                                            :ref:`Single Crystal Reflections
866                                            <XtalRefl_table>`
867                                            description.
868
869Instrument Parameters       \\               (list) containing two dicts where the possible
870                                            keys in each dict are listed below. The value
871                                            for most items is a list containing two values:
872                                            the initial value, the current value.
873                                            The first and second
874                                            values are floats unless otherwise noted.
875\\                           Lam             (two floats) Specifies a wavelength in :math:`\\AA`
876\\                           Type            (two str values) Histogram type :
877                                            * 'SXC' for constant wavelength x-ray
878                                            * 'SNC' for constant wavelength neutron
879                                            * 'SNT' for time of flight neutron
880\\                           InstrName       (str) A name for the instrument, used in preparing a CIF
881wtFactor                    \\               (float) A weighting factor to increase or decrease
882                                            the leverage of data in the histogram.
883                                            A value of 1.0 weights the data with their
884                                            standard uncertainties and a larger value
885                                            increases the weighting of the data (equivalent
886                                            to decreasing the uncertainties).
887
888hId                         \\               (int) The number assigned to the histogram when
889                                            the project is loaded or edited (can change)
890ranId                       \\               (int) A random number id for the histogram
891                                            that does not change
892======================  ===============     ====================================================
893
894.. _XtalRefl_table:
895
896.. index::
897   single: Single Crystal reflection object description
898   single: Data object descriptions; Single Crystal Reflections
899
900Single Crystal Reflection Data Structure
901----------------------------------------
902
903For every single crystal a histogram, the ``'Data'`` item contains
904the structure factors as an np.array in item `'RefList'`.
905The columns in that array are documented below.
906
907.. tabularcolumns:: |l|p{4in}|
908
909==========  ====================================================
910  index         explanation
911==========  ====================================================
912 0,1,2          (float) h,k,l
913 3              (int) multiplicity
914 4              (float) d-space, :math:`\\AA`
915 5              (float) :math:`F_{obs}^2`
916 6              (float) :math:`\\sigma(F_{obs}^2)`
917 7              (float) :math:`F_{calc}^2`
918 8              (float) :math:`F_{obs}^2T`
919 9              (float) :math:`F_{calc}^2T`
920 10             (float) reflection phase, in degrees
921 11             (float) intensity correction for reflection, this times
922                :math:`F_{obs}^2` or :math:`F_{calc}^2`
923                gives Iobs or Icalc
924==========  ====================================================
925
926.. _Image_table:
927
928.. index::
929   image: Image data object description
930   image: Image object descriptions
931
932Image Data Structure
933--------------------
934
935Every 2-dimensional image is stored in the GSAS-II data tree
936with a top-level entry named beginning with the string "IMG ". The
937image data are directly associated with that tree item and there
938are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
939and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
940load this information into a dictionary where the child tree name is
941used as a key, and the information in the main entry is assigned
942a key of ``Data``, as outlined below.
943
944.. tabularcolumns:: |l|l|p{4in}|
945
946======================  ======================  ====================================================
947  key                      sub-key              explanation
948======================  ======================  ====================================================
949Comments                    \\                   (list of str) Text strings extracted from the original image data
950                                                header or a metafile. These cannot be changed by
951                                                the user; it may be empty.
952Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
953                                                value. Accomodates
954                                                detector orientations other than with the detector
955                                                X-axis
956                                                horizontal.
957\\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
958                                                during image integration multiplied by value. It must have the same size/shape as
959                                                the integrated image. NB: value < 0 for subtraction.
960\\                           calibrant           (str) The material used for determining the position/orientation
961                                                of the image. The data is obtained from :func:`ImageCalibrants`
962                                                and UserCalibrants.py (supplied by user).
963\\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
964\\                           calibskip           (int) The number of expected diffraction lines skipped during the last
965                                                calibration run.
966\\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
967                                                strikes the detector plane as determined by calibration. This point
968                                                does not have to be within the limits of the detector boundaries.
969\\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
970                                                of the image is at the center line otherwise it is at the leading edge.
971\\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
972\\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
973                                                calibration calculations. See pixLimit for details as how point is found.
974\\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
975                                                ring offset at higher angles. Optionally determined by calibration.
976\\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
977\\                           distance            (float) The distance (mm) from sample to detector plane.
978\\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
979                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
980                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
981                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
982                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
983\\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
984\\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
985\\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
986                                                Required for texture calculations.
987\\                           invert_x            (bool) If True display the image with the x-axis inverted.
988\\                           invert_y            (bool) If True display the image with the y-axis inverted.
989\\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
990\\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
991\\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
992                                                intensities obtained during integration.
993\\                           outAzimuths         (int) The number of azimuth pie slices.
994\\                           outChannels         (int) The number of 2-theta steps.
995\\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
996\\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
997                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
998                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
999                                                Locations are used to construct rings of points for calibration calcualtions.
1000\\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
1001                                                integration using value.
1002\\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
1003                                                diffraction ring with the same d-spacing (dsp)
1004\\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
1005                                                selected by the user,
1006\\                           Range               (list) The minimum & maximum values of the image
1007\\                           rotation            (float) The angle between the x-axis and the vector about which the
1008                                                detector is tilted. Constrained to -180 to 180 deg.
1009\\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
1010                                                calculations.
1011\\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
1012                                                to cause correction to be applied.
1013\\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
1014\\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
1015\\                           showLines           (bool) If True then isplay the integration limits to be used.
1016\\                           size                (list:int) The number of pixels on the image x & y axes
1017\\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
1018\\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
1019\\                           wavelength          (float) The radiation wavelength (:math:`\\AA`) as entered by the user
1020                                                (or someday obtained from the image header).
1021Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
1022                                                to be excluded from integration
1023\\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
1024                                                of which is excluded from recalibration and integration. Only one frame is allowed.
1025\\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
1026                                                from integration.
1027\\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
1028                                                to be excluded from integration.
1029\\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
1030                                                to be excluded from integration.
1031\\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
1032                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
1033\\                           SpotMask            (dict: int & array)
1034                                                'esdMul'(int) number of standard deviations above mean ring intensity to mask
1035                                                'spotMask' (bool array) the spot mask for every pixel in image         
1036
1037Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
1038\\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
1039                                                These will be restricted by space group symmetry; result of strain fit refinement.
1040\\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
1041\\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
1042                                                and are used to determine the strain tensor.
1043                                                The dictionary items are:
1044                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
1045                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
1046                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
1047                                                'Esig': (list: float) Esds for Emat from fitting.
1048                                                'pixLimit': (int) Search range to find highest point on ring for each data point
1049                                                'cutoff': (float) I/Ib cutoff for searching.
1050                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
1051                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
1052                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
1053
1054======================  ======================  ====================================================
1055
1056.. _parmDict_table:
1057
1058.. index::
1059   single: Parameter dictionary
1060
1061Parameter Dictionary
1062-------------------------
1063
1064The parameter dictionary contains all of the variable parameters for the refinement.
1065The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
1066It is prepared in two ways. When loaded from the tree
1067(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
1068:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
1069the values are lists with two elements: ``[value, refine flag]``
1070
1071When loaded from the GPX file (in
1072:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
1073dict is the actual parameter value (usually a float, but sometimes a
1074letter or string flag value (such as I or A for iso/anisotropic).
1075
1076Texture implementation
1077------------------------------
1078
1079There are two different places where texture can be treated in GSAS-II.
1080One is for mitigating the effects of texture in a structural refinement.
1081The other is for texture characterization.
1082
1083For reducing the effect of texture in a structural refinement
1084there are entries labeled preferred orientation in each phase's
1085data tab. Two different
1086approaches can be used for this, the March-Dollase model and
1087spherical harmonics.
1088For the March-Dollase model, one axis in reciprocal space is designated as
1089unique (defaulting to the 001 axis) and reflections are corrected
1090according to the angle they make with this axis depending on
1091the March-Dollase ratio. (If unity, no correction is made).
1092The ratio can be greater than one or less than one depending on if
1093crystallites oriented along the designated axis are
1094overrepresented or underrepresented. For most crystal systems there is an
1095obvious choice for the direction of the unique axis and then only a single
1096term needs to be refined. If the number is close to 1, then the correction
1097is not needed.
1098
1099The second method for reducing the effect of texture in a structural
1100refinement is to create a probability surface as an expansion in
1101terms spherical harmonic functions. Only functions consistent with
1102cylindrical diffraction suymmetry and having texture symmetry
1103consistent with the Laue class of phase are used and are allowed,
1104so the higher the symmetry
1105the fewer terms that are available for a given spherical harmonics order.
1106For use of this correction, select the lowest order that provides
1107refinable terms and perform a refinement. If the texture index remains close to
1108one, then the correction is not needed. If a significant improvement is
1109noted in the profile Rwp, one may wish to see if a higher order expansion
1110gives an even larger improvement.
1111
1112To characterize texture in a material, one needs data collected with the
1113sample at multiple orientations or, for TOF, with detectors at multiple
1114locations around the sample. In this case the detector orientation is given in
1115each histogram's Sample Parameters and the sample's orientation is described
1116with the Euler angles specifed on the phase's Texture tab, which is also
1117where the texture type (cylindrical, rolling,...) and the sherical
1118harmonic order is selected. This should not be used with a single dataset and
1119should not be used if the preferred orientations corrections are used.
1120
1121The coordinate system used for texture characterization is defined where
1122the sample coordinates (Psi, gamma) are defined with an instrument coordinate
1123system (I, J, K) such that I is normal to the diffraction plane and J is coincident with the
1124direction of the incident radiation beam pointing away from the source. We further define
1125a standard set of right-handed goniometer eulerian angles (Omega, Chi, Phi) so that Omega and Phi are
1126rotations about I and Chi is a rotation about J when Omega, Chi, Phi = 0. Finally, as the sample
1127may be mounted so that the sample coordinate system (Is, Js, Ks) does not coincide with
1128the instrument coordinate system (I, J, K), we define three eulerian sample rotation angles
1129(Omega-s, Chi-s, Phi-s) that describe the rotation from (I, J, K) to (Is, Js, Ks). The sample rotation
1130angles are defined so that with the goniometer angles at zero Omega-s and Phi-s are rotations
1131about I and Chi-s is a rotation about J.
1132
1133ISODISTORT implementation
1134------------------------------
1135
1136CIFs prepared with the ISODISTORT web site
1137https://stokes.byu.edu/iso/isodistort_version5.6.1/isodistort.php
1138[B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions." J. Appl. Cryst. 39, 607-614 (2006).]
1139can be read into GSAS-II using import CIF. This will cause constraints to be established for structural distortion modes read from the CIF.
1140At present, of the five types of modes  only displacive(``_iso_displacivemode``...) and occupancy (``_iso_occupancymode``...) are processed. Not yet processed: ``_iso_magneticmode``..., ``_iso_rotationalmode``... & ``_iso_strainmode``...
1141
1142The CIF importer :mod:`G2phase_CIF` implements class :class:`G2phase_CIF.CIFPhaseReader` which offers two methods associated with ISODISTORT (ID) input. Method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_test`
1143checks to see if a CIF block contains the loops with ``_iso_displacivemode_label`` or  ``_iso_occupancymode_label`` items.
1144If so, method :meth:`G2phase_CIF.CIFPhaseReader.ISODISTORT_proc` is called to read and interpret them.
1145The results are placed into the reader object's ``.Phase`` class variable as a dict item with key ``'ISODISTORT'``.
1146
1147Note that each mode ID has a long label with a name such as  Pm-3m[1/2,1/2,1/2]R5+(a,a,0)[La:b:dsp]T1u(a). Function :func:`G2phase_CIF.ISODISTORT_shortLbl` is used to create a short name for this,
1148such as R5_T1u(a) which is made unique by addition of _n if the short name is duplicated.
1149As each mode is processed, a constraint corresponding to that mode is
1150created and is added to list in the reader object's ``.Constraints`` class variable. Items placed into that list can either be a list, which corresponds to a function (new var) type :ref:`constraint definition <Constraints_table>` entry, or an item can be a dict, which provides help information for each constraint.
1151
1152------------------------------
1153Displacive modes
1154------------------------------
1155
1156The coordinate variables, as named by ISODISTORT, are placed in
1157``.Phase['ISODISTORT']['IsoVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2VarList']``. The mode variables,
1158as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['IsoModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2ModeList']``.
1159[Use ``str(G2VarObj)`` to get the variable name from the G2VarObj object, but note that the phase number, *n*, for the prefix "*n*::" cannot be determined as the phase number is not yet assigned.]
1160
1161Displacive modes are a bit complex in that they relate to delta displacements, relative to an offset value for each coordinate, and because the modes are normalized, while GSAS-II also uses displacements, but these are added to the coordinates after each refinement cycle and the delta values are set to zero. ISODISTORT uses fixed offsets (subtracted from the actual position to obtain the delta values) that are taken from ``_iso_coordinate_formula`` and these are placed in ``.Phase['ISODISTORT']['ParentStructure]`` (keyed by atom label). The normalization factors (which the delta values are divided by) are taken from ``_iso_displacivemodenorm_value`` and are placed in ``.Phase['ISODISTORT']['NormList']`` in the same order as as ``...['IsoModeList']`` and
1162``...['G2ModeList']``.
1163
1164The CIF contains a sparse matrix, from the ``loop_`` containing
1165``_iso_displacivemodematrix_value`` which provides the equations for determining the mode values from the coordinates, that matrix is placed in ``.Phase['ISODISTORT']['Mode2VarMatrix']``. The matrix is inverted to produce
1166``.Phase['ISODISTORT']['Var2ModeMatrix']``, which determines how to compute the
1167mode values from the delta coordinate values. These values are used for the
1168in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1169values, the latter with s.u. values.
1170
1171
1172------------------------------
1173Occupancy modes
1174------------------------------
1175
1176
1177The delta occupancy variables, as named by ISODISTORT, are placed in
1178``.Phase['ISODISTORT']['OccVarList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2OccVarList']``. The mode variables, as named by ISODISTORT, are placed in ``.Phase['ISODISTORT']['OccModeList']`` and the corresponding :class:`GSASIIobj.G2VarObj` objects for each are placed in ``.Phase['ISODISTORT']['G2OccModeList']``.
1179
1180Occupancy modes, like Displacive modes, are also refined as delta values.  However, GSAS-II directly refines the fractional occupancies.
1181Offset values for each atom, are taken from ``_iso_occupancy_formula`` and are placed in
1182``.Phase['ISODISTORT']['ParentOcc]``.
1183(Offset values are subtracted from the actual position to obtain the delta values.)
1184Modes are normalized (where the mode values are divided by the normalization factor)
1185are taken from ``_iso_occupancymodenorm_value`` and are placed in ``.Phase['ISODISTORT']['OccNormList']`` in the same order as as ``...['OccModeList']`` and
1186``...['G2OccModeList']``.
1187
1188The CIF contains a sparse matrix, from the ``loop_`` containing
1189``_iso_occupancymodematrix_value``, which provides the equations for determining the mode values from the coordinates. That matrix is placed in ``.Phase['ISODISTORT']['Occ2VarMatrix']``. The matrix is inverted to produce
1190``.Phase['ISODISTORT']['Var2OccMatrix']``, which determines how to compute the
1191mode values from the delta coordinate values.
1192
1193
1194------------------------------
1195Mode Computations
1196------------------------------
1197
1198Constraints are processed after the CIF has been read in
1199:meth:`GSASIIdataGUI.GSASII.OnImportPhase` or 
1200:meth:`GSASIIscriptable.G2Project.add_phase` by moving them from the reader
1201object's ``.Constraints`` class variable to
1202the Constraints tree entry's ['Phase'] list (for list items defining constraints) or
1203the Constraints tree entry's ['_Explain'] dict (for dict items defining constraint help information)
1204
1205The information in ``.Phase['ISODISTORT']`` is used
1206in :func:`GSASIIconstrGUI.ShowIsoDistortCalc` which shows coordinate and mode
1207values, the latter with s.u. values. This can be called from the Constraints and Phase/Atoms tree items.
1208
1209Before each refinement, constraints are processed as
1210:ref:`described elsewhere <Constraints_processing>`. After a refinement
1211is complete, :func:`GSASIImapvars.PrintIndependentVars` shows the
1212shifts and s.u.'s on the refined modes, using GSAS-II values, but
1213:func:`GSASIIstrIO.PrintISOmodes` prints the ISODISTORT modes as computed
1214in the web site.
1215
1216
1217.. _ParameterLimits:
1218
1219.. index::
1220   single: Parameter limits
1221
1222Parameter Limits
1223------------------------------
1224
1225One of the most often requested "enhancements" for GSAS-II would be the inclusion
1226of constraints to force parameters such as occupancies or Uiso values to stay within
1227expected ranges. While it is possible for users to supply their own restraints that would
1228perform this by supplying an appropriate expression with the "General" restraints, the
1229GSAS-II authors do not feel that use of restraints or constraints are a good solution for
1230this common problem where parameters refine to non-physical values. This is because when
1231this occurs, most likely one of the following cases is occurring:
1232
1233#. there is a significant problem
1234   with the model, for example for an x-ray fit if an O atom is placed where a S is actually
1235   present, the Uiso will refine artificially small or the occupancy much larger than unity
1236   to try to compensate for the missing electrons; or
1237 
1238#. the data are simply insensitive
1239   to the parameter or combination of parameters, for example unless very high-Q data
1240   are included, the effects of a occupancy and Uiso value can have compensating effects,
1241   so an assumption must be made; likewise, with neutron data natural-abundance V atoms
1242   are nearly invisible due to weak coherent scattering. No parameters can be fit for a
1243   V atom with neutrons.
1244
1245#. the parameter is non-physical (such as a negative Uiso value) but within
1246   two sigma (sigma = standard uncertainty, aka e.s.d.) of a reasonable value,
1247   in which case the
1248   value is not problematic as it is experimentally indistinguishable from an
1249   expected value. 
1250
1251#. there is a systematic problem with the data (experimental error)
1252
1253In all these cases, this situation needs to be reviewed by a crystallographer to decide
1254how to best determine a structural model for these data. An implementation with a constraint
1255or restraint is likely to simply hide the problem from the user, making it more probable
1256that a poor model choice is obtained.
1257
1258What GSAS-II does implement is to allow users to specify ranges for parameters
1259that works by disabling
1260refinement of parameters that refine beyond either a lower limit or an upper limit, where
1261either or both may be optionally specified. Parameters limits are specified in the Controls
1262tree entry in dicts named as ``Controls['parmMaxDict']`` and ``Controls['parmMinDict']``, where
1263the keys are :class:`G2VarObj` objects corresponding to standard GSAS-II variable
1264(see :func:`getVarDescr` and :func:`CompileVarDesc`) names, where a
1265wildcard ('*') may optionally be used for histogram number or atom number
1266(phase number is intentionally not  allowed as a wildcard as it makes little sense
1267to group the same parameter together different phases). Note
1268that :func:`prmLookup` is used to see if a name matches a wildcard. The upper or lower limit
1269is placed into these dicts as a float value. These values can be edited using the window
1270created by the Calculate/"View LS parms" menu command or in scripting with the
1271:meth:`GSASIIscriptable.G2Project.set_Controls` function.
1272In the GUI, a checkbox labeled "match all histograms/atoms" is used to insert a wildcard
1273into the appropriate part of the variable name.
1274
1275When a refinement is conducted, routine :func:`GSASIIstrMain.dropOOBvars` is used to
1276find parameters that have refined to values outside their limits. If this occurs, the parameter
1277is set to the limiting value and the variable name is added to a list of frozen variables
1278(as a :class:`G2VarObj` objects) kept in a list in the
1279``Controls['parmFrozen']`` dict. In a sequential refinement, this is kept separate for
1280each histogram as a list in
1281``Controls['parmFrozen'][histogram]`` (where the key is the histogram name) or as a list in
1282``Controls['parmFrozen']['FrozenList']`` for a non-sequential fit.
1283This allows different variables
1284to be frozen in each section of a sequential fit.
1285Frozen parameters are not included in refinements through removal from the
1286list of parameters to be refined (``varyList``) in :func:`GSASIIstrMain.Refine` or
1287:func:`GSASIIstrMain.SeqRefine`.
1288The data window for the Controls tree item shows the number of Frozen variables and
1289the individual variables can be viewed with the Calculate/"View LS parms" menu window or
1290obtained with :meth:`GSASIIscriptable.G2Project.get_Frozen`.
1291Once a variable is frozen, it will not be refined in any
1292future refinements unless the the variable is removed (manually) from the list. This can also
1293be done with the Calculate/"View LS parms" menu window or
1294:meth:`GSASIIscriptable.G2Project.set_Frozen`.
1295
1296
1297.. seealso::
1298  :class:`G2VarObj`
1299  :func:`getVarDescr`
1300  :func:`CompileVarDesc`
1301  :func:`prmLookup`
1302  :class:`GSASIIctrlGUI.ShowLSParms`
1303  :class:`GSASIIctrlGUI.VirtualVarBox`
1304  :func:`GSASIIstrIO.SetUsedHistogramsAndPhases`
1305  :func:`GSASIIstrIO.SaveUpdatedHistogramsAndPhases`
1306  :func:`GSASIIstrIO.SetSeqResult`
1307  :func:`GSASIIstrMain.dropOOBvars`
1308  :meth:`GSASIIscriptable.G2Project.set_Controls`
1309  :meth:`GSASIIscriptable.G2Project.get_Frozen`
1310  :meth:`GSASIIscriptable.G2Project.set_Frozen`
1311
1312*Classes and routines*
1313----------------------
1314
1315'''
1316from __future__ import division, print_function
1317import platform
1318import re
1319import random as ran
1320import sys
1321import os.path as ospath
1322if '2' in platform.python_version_tuple()[0]:
1323    import cPickle
1324else:
1325    import pickle as cPickle
1326import GSASIIpath
1327import GSASIImath as G2mth
1328import GSASIIspc as G2spc
1329import numpy as np
1330
1331GSASIIpath.SetVersionNumber("$Revision: 4823 $")
1332
1333DefaultControls = {
1334    'deriv type':'analytic Hessian',
1335    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
1336    'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
1337    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
1338    'Author':'no name',
1339    'FreePrm1':'Sample humidity (%)',
1340    'FreePrm2':'Sample voltage (V)',
1341    'FreePrm3':'Applied load (MN)',
1342    'ShowCell':False,
1343    }
1344'''Values to be used as defaults for the initial contents of the ``Controls``
1345data tree item.
1346'''
1347def StripUnicode(string,subs='.'):
1348    '''Strip non-ASCII characters from strings
1349
1350    :param str string: string to strip Unicode characters from
1351    :param str subs: character(s) to place into string in place of each
1352      Unicode character. Defaults to '.'
1353
1354    :returns: a new string with only ASCII characters
1355    '''
1356    s = ''
1357    for c in string:
1358        if ord(c) < 128:
1359            s += c
1360        else:
1361            s += subs
1362    return s
1363#    return s.encode('ascii','replace')
1364
1365def MakeUniqueLabel(lbl,labellist):
1366    '''Make sure that every a label is unique against a list by adding
1367    digits at the end until it is not found in list.
1368
1369    :param str lbl: the input label
1370    :param list labellist: the labels that have already been encountered
1371    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
1372      ``_10-99``, etc.) appended at the end
1373    '''
1374    lbl = StripUnicode(lbl.strip(),'_')
1375    if not lbl: # deal with a blank label
1376        lbl = '_1'
1377    if lbl not in labellist:
1378        labellist.append(lbl)
1379        return lbl
1380    i = 1
1381    prefix = lbl
1382    if '_' in lbl:
1383        prefix = lbl[:lbl.rfind('_')]
1384        suffix = lbl[lbl.rfind('_')+1:]
1385        try:
1386            i = int(suffix)+1
1387        except: # suffix could not be parsed
1388            i = 1
1389            prefix = lbl
1390    while prefix+'_'+str(i) in labellist:
1391        i += 1
1392    else:
1393        lbl = prefix+'_'+str(i)
1394        labellist.append(lbl)
1395    return lbl
1396
1397PhaseIdLookup = {}
1398'''dict listing phase name and random Id keyed by sequential phase index as a str;
1399best to access this using :func:`LookupPhaseName`
1400'''
1401PhaseRanIdLookup = {}
1402'''dict listing phase sequential index keyed by phase random Id;
1403best to access this using :func:`LookupPhaseId`
1404'''
1405HistIdLookup = {}
1406'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
1407best to access this using :func:`LookupHistName`
1408'''
1409HistRanIdLookup = {}
1410'''dict listing histogram sequential index keyed by histogram random Id;
1411best to access this using :func:`LookupHistId`
1412'''
1413AtomIdLookup = {}
1414'''dict listing for each phase index as a str, the atom label and atom random Id,
1415keyed by atom sequential index as a str;
1416best to access this using :func:`LookupAtomLabel`
1417'''
1418AtomRanIdLookup = {}
1419'''dict listing for each phase the atom sequential index keyed by atom random Id;
1420best to access this using :func:`LookupAtomId`
1421'''
1422ShortPhaseNames = {}
1423'''a dict containing a possibly shortened and when non-unique numbered
1424version of the phase name. Keyed by the phase sequential index.
1425'''
1426ShortHistNames = {}
1427'''a dict containing a possibly shortened and when non-unique numbered
1428version of the histogram name. Keyed by the histogram sequential index.
1429'''
1430
1431#VarDesc = {}  # removed 1/30/19 BHT as no longer needed (I think)
1432#''' This dictionary lists descriptions for GSAS-II variables,
1433#as set in :func:`CompileVarDesc`. See that function for a description
1434#for how keys and values are written.
1435#'''
1436
1437reVarDesc = {}
1438''' This dictionary lists descriptions for GSAS-II variables where
1439keys are compiled regular expressions that will match the name portion
1440of a parameter name. Initialized in :func:`CompileVarDesc`.
1441'''
1442
1443reVarStep = {}
1444''' This dictionary lists the preferred step size for numerical
1445derivative computation w/r to a GSAS-II variable. Keys are compiled
1446regular expressions and values are the step size for that parameter.
1447Initialized in :func:`CompileVarDesc`.
1448'''
1449# create a default space group object for P1; N.B. fails when building documentation
1450try:
1451    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1452except:
1453    pass
1454
1455def GetPhaseNames(fl):
1456    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1457    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1458
1459    :param file fl: opened .gpx file
1460    :return: list of phase names
1461    '''
1462    PhaseNames = []
1463    while True:
1464        try:
1465            data = cPickle.load(fl)
1466        except EOFError:
1467            break
1468        datum = data[0]
1469        if 'Phases' == datum[0]:
1470            for datus in data[1:]:
1471                PhaseNames.append(datus[0])
1472    fl.seek(0)          #reposition file
1473    return PhaseNames
1474
1475def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1476    '''Create a new phase dict with default values for various parameters
1477
1478    :param str Name: Name for new Phase
1479
1480    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1481      defaults to data for P 1
1482
1483    :param list cell: unit cell parameter list; defaults to
1484      [1.0,1.0,1.0,90.,90,90.,1.]
1485
1486    '''
1487    if SGData is None: SGData = P1SGData
1488    if cell is None: cell=[1.0,1.0,1.0,90.,90.,90.,1.]
1489    phaseData = {
1490        'ranId':ran.randint(0,sys.maxsize),
1491        'General':{
1492            'Name':Name,
1493            'Type':'nuclear',
1494            'Modulated':False,
1495            'AtomPtrs':[3,1,7,9],
1496            'SGData':SGData,
1497            'Cell':[False,]+cell,
1498            'Pawley dmin':1.0,
1499            'Data plot type':'None',
1500            'SH Texture':{
1501                'Order':0,
1502                'Model':'cylindrical',
1503                'Sample omega':[False,0.0],
1504                'Sample chi':[False,0.0],
1505                'Sample phi':[False,0.0],
1506                'SH Coeff':[False,{}],
1507                'SHShow':False,
1508                'PFhkl':[0,0,1],
1509                'PFxyz':[0,0,1],
1510                'PlotType':'Pole figure',
1511                'Penalty':[['',],0.1,False,1.0]}},
1512        'Atoms':[],
1513        'Drawing':{},
1514        'Histograms':{},
1515        'Pawley ref':[],
1516        'RBModels':{},
1517        }
1518    if Super and Super.get('Use',False):
1519        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1520        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])[1]
1521        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1522
1523    return phaseData
1524
1525def ReadCIF(URLorFile):
1526    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1527    (from James Hester).
1528    The open routine gets confused with DOS names that begin with a letter and colon
1529    "C:\\dir\" so this routine will try to open the passed name as a file and if that
1530    fails, try it as a URL
1531
1532    :param str URLorFile: string containing a URL or a file name. Code will try first
1533      to open it as a file and then as a URL.
1534
1535    :returns: a PyCifRW CIF object.
1536    '''
1537    import CifFile as cif # PyCifRW from James Hester
1538
1539    # alternate approach:
1540    #import urllib
1541    #ciffile = 'file:'+urllib.pathname2url(filename)
1542
1543    try:
1544        fp = open(URLorFile,'r')
1545        cf = cif.ReadCif(fp)
1546        fp.close()
1547        return cf
1548    except IOError:
1549        return cif.ReadCif(URLorFile)
1550
1551def TestIndexAll():
1552    '''Test if :func:`IndexAllIds` has been called to index all phases and
1553    histograms (this is needed before :func:`G2VarObj` can be used.
1554
1555    :returns: Returns True if indexing is needed.
1556    '''
1557    if PhaseIdLookup or AtomIdLookup or HistIdLookup:
1558        return False
1559    return True
1560       
1561def IndexAllIds(Histograms,Phases):
1562    '''Scan through the used phases & histograms and create an index
1563    to the random numbers of phases, histograms and atoms. While doing this,
1564    confirm that assigned random numbers are unique -- just in case lightning
1565    strikes twice in the same place.
1566
1567    Note: this code assumes that the atom random Id (ranId) is the last
1568    element each atom record.
1569
1570    This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
1571    (which loads the histograms and phases from a GPX file),
1572    :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
1573    (which loads the histograms and phases from the data tree.) and
1574    :meth:`GSASIIconstrGUI.UpdateConstraints`
1575    (which displays & edits the constraints in a GUI)
1576
1577    TODO: do we need a lookup for rigid body variables?
1578    '''
1579    # process phases and atoms
1580    PhaseIdLookup.clear()
1581    PhaseRanIdLookup.clear()
1582    AtomIdLookup.clear()
1583    AtomRanIdLookup.clear()
1584    ShortPhaseNames.clear()
1585    for ph in Phases:
1586        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1587        ranId = Phases[ph]['ranId']
1588        while ranId in PhaseRanIdLookup:
1589            # Found duplicate random Id! note and reassign
1590            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1591            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1592        pId = str(Phases[ph]['pId'])
1593        PhaseIdLookup[pId] = (ph,ranId)
1594        PhaseRanIdLookup[ranId] = pId
1595        shortname = ph  #[:10]
1596        while shortname in ShortPhaseNames.values():
1597            shortname = ph[:8] + ' ('+ pId + ')'
1598        ShortPhaseNames[pId] = shortname
1599        AtomIdLookup[pId] = {}
1600        AtomRanIdLookup[pId] = {}
1601        for iatm,at in enumerate(Phases[ph]['Atoms']):
1602            ranId = at[cia+8]
1603            while ranId in AtomRanIdLookup[pId]: # check for dups
1604                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1605                at[cia+8] = ranId = ran.randint(0,sys.maxsize)
1606            AtomRanIdLookup[pId][ranId] = str(iatm)
1607            if Phases[ph]['General']['Type'] == 'macromolecular':
1608                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1609            else:
1610                label = at[ct-1]
1611            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1612    # process histograms
1613    HistIdLookup.clear()
1614    HistRanIdLookup.clear()
1615    ShortHistNames.clear()
1616    for hist in Histograms:
1617        ranId = Histograms[hist]['ranId']
1618        while ranId in HistRanIdLookup:
1619            # Found duplicate random Id! note and reassign
1620            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1621            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxsize)
1622        hId = str(Histograms[hist]['hId'])
1623        HistIdLookup[hId] = (hist,ranId)
1624        HistRanIdLookup[ranId] = hId
1625        shortname = hist[:15]
1626        while shortname in ShortHistNames.values():
1627            shortname = hist[:11] + ' ('+ hId + ')'
1628        ShortHistNames[hId] = shortname
1629
1630def LookupAtomId(pId,ranId):
1631    '''Get the atom number from a phase and atom random Id
1632
1633    :param int/str pId: the sequential number of the phase
1634    :param int ranId: the random Id assigned to an atom
1635
1636    :returns: the index number of the atom (str)
1637    '''
1638    if not AtomRanIdLookup:
1639        raise Exception('Error: LookupAtomId called before IndexAllIds was run')
1640    if pId is None or pId == '':
1641        raise KeyError('Error: phase is invalid (None or blank)')
1642    pId = str(pId)
1643    if pId not in AtomRanIdLookup:
1644        raise KeyError('Error: LookupAtomId does not have phase '+pId)
1645    if ranId not in AtomRanIdLookup[pId]:
1646        raise KeyError('Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']')
1647    return AtomRanIdLookup[pId][ranId]
1648
1649def LookupAtomLabel(pId,index):
1650    '''Get the atom label from a phase and atom index number
1651
1652    :param int/str pId: the sequential number of the phase
1653    :param int index: the index of the atom in the list of atoms
1654
1655    :returns: the label for the atom (str) and the random Id of the atom (int)
1656    '''
1657    if not AtomIdLookup:
1658        raise Exception('Error: LookupAtomLabel called before IndexAllIds was run')
1659    if pId is None or pId == '':
1660        raise KeyError('Error: phase is invalid (None or blank)')
1661    pId = str(pId)
1662    if pId not in AtomIdLookup:
1663        raise KeyError('Error: LookupAtomLabel does not have phase '+pId)
1664    if index not in AtomIdLookup[pId]:
1665        raise KeyError('Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']')
1666    return AtomIdLookup[pId][index]
1667
1668def LookupPhaseId(ranId):
1669    '''Get the phase number and name from a phase random Id
1670
1671    :param int ranId: the random Id assigned to a phase
1672    :returns: the sequential Id (pId) number for the phase (str)
1673    '''
1674    if not PhaseRanIdLookup:
1675        raise Exception('Error: LookupPhaseId called before IndexAllIds was run')
1676    if ranId not in PhaseRanIdLookup:
1677        raise KeyError('Error: LookupPhaseId does not have ranId '+str(ranId))
1678    return PhaseRanIdLookup[ranId]
1679
1680def LookupPhaseName(pId):
1681    '''Get the phase number and name from a phase Id
1682
1683    :param int/str pId: the sequential assigned to a phase
1684    :returns:  (phase,ranId) where phase is the name of the phase (str)
1685      and ranId is the random # id for the phase (int)
1686    '''
1687    if not PhaseIdLookup:
1688        raise Exception('Error: LookupPhaseName called before IndexAllIds was run')
1689    if pId is None or pId == '':
1690        raise KeyError('Error: phase is invalid (None or blank)')
1691    pId = str(pId)
1692    if pId not in PhaseIdLookup:
1693        raise KeyError('Error: LookupPhaseName does not have index '+pId)
1694    return PhaseIdLookup[pId]
1695
1696def LookupHistId(ranId):
1697    '''Get the histogram number and name from a histogram random Id
1698
1699    :param int ranId: the random Id assigned to a histogram
1700    :returns: the sequential Id (hId) number for the histogram (str)
1701    '''
1702    if not HistRanIdLookup:
1703        raise Exception('Error: LookupHistId called before IndexAllIds was run')
1704    if ranId not in HistRanIdLookup:
1705        raise KeyError('Error: LookupHistId does not have ranId '+str(ranId))
1706    return HistRanIdLookup[ranId]
1707
1708def LookupHistName(hId):
1709    '''Get the histogram number and name from a histogram Id
1710
1711    :param int/str hId: the sequential assigned to a histogram
1712    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1713      and ranId is the random # id for the histogram (int)
1714    '''
1715    if not HistIdLookup:
1716        raise Exception('Error: LookupHistName called before IndexAllIds was run')
1717    if hId is None or hId == '':
1718        raise KeyError('Error: histogram is invalid (None or blank)')
1719    hId = str(hId)
1720    if hId not in HistIdLookup:
1721        raise KeyError('Error: LookupHistName does not have index '+hId)
1722    return HistIdLookup[hId]
1723
1724def fmtVarDescr(varname):
1725    '''Return a string with a more complete description for a GSAS-II variable
1726
1727    :param str varname: A full G2 variable name with 2 or 3 or 4
1728       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1729
1730    :returns: a string with the description
1731    '''
1732    s,l = VarDescr(varname)
1733    return s+": "+l
1734
1735def VarDescr(varname):
1736    '''Return two strings with a more complete description for a GSAS-II variable
1737
1738    :param str name: A full G2 variable name with 2 or 3 or 4
1739       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1740
1741    :returns: (loc,meaning) where loc describes what item the variable is mapped
1742      (phase, histogram, etc.) and meaning describes what the variable does.
1743    '''
1744
1745    # special handling for parameter names without a colon
1746    # for now, assume self-defining
1747    if varname.find(':') == -1:
1748        return "Global",varname
1749
1750    l = getVarDescr(varname)
1751    if not l:
1752        return ("invalid variable name ("+str(varname)+")!"),""
1753#        return "invalid variable name!",""
1754
1755    if not l[-1]:
1756        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1757
1758    if len(l) == 3:         #SASD variable name!
1759        s = 'component:'+l[1]
1760        return s,l[-1]
1761    s = ""
1762    if l[0] is not None and l[1] is not None: # HAP: keep short
1763        if l[2] == "Scale": # fix up ambigous name
1764            l[5] = "Phase fraction"
1765        if l[0] == '*':
1766            lbl = 'Seq. ref.'
1767        else:
1768            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1769        if l[1] == '*':
1770            hlbl = 'Seq. ref.'
1771        else:
1772            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1773        if hlbl[:4] == 'HKLF':
1774            hlbl = 'Xtl='+hlbl[5:]
1775        elif hlbl[:4] == 'PWDR':
1776            hlbl = 'Pwd='+hlbl[5:]
1777        else:
1778            hlbl = 'Hist='+hlbl
1779        s = "Ph="+str(lbl)+" * "+str(hlbl)
1780    else:
1781        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1782            l[5] = "Scale factor"
1783        if l[2] == 'Back': # background parameters are "special", alas
1784            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1785            l[-1] += ' #'+str(l[3])
1786        elif l[4] is not None: # rigid body parameter or modulation parm
1787            lbl = ShortPhaseNames.get(l[0],'phase?')
1788            if 'RB' in l[2]:    #rigid body parm
1789                s = "RB body #"+str(l[3])+" (type "+str(l[4])+") in "+str(lbl) + ','
1790            else: #modulation parm
1791                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1792        elif l[3] is not None: # atom parameter,
1793            lbl = ShortPhaseNames.get(l[0],'phase?')
1794            try:
1795                albl = LookupAtomLabel(l[0],l[3])[0]
1796            except KeyError:
1797                albl = 'Atom?'
1798            s = "Atom "+str(albl)+" in "+str(lbl)
1799        elif l[0] == '*':
1800            s = "All phases "
1801        elif l[0] is not None:
1802            lbl = ShortPhaseNames.get(l[0],'phase?')
1803            s = "Phase "+str(lbl)
1804        elif l[1] == '*':
1805            s = 'All hists'
1806        elif l[1] is not None:
1807            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1808            if hlbl[:4] == 'HKLF':
1809                hlbl = 'Xtl='+hlbl[5:]
1810            elif hlbl[:4] == 'PWDR':
1811                hlbl = 'Pwd='+hlbl[5:]
1812            else:
1813                hlbl = 'Hist='+hlbl
1814            s = str(hlbl)
1815    if not s:
1816        s = 'Global'
1817    return s,l[-1]
1818
1819def getVarDescr(varname):
1820    '''Return a short description for a GSAS-II variable
1821
1822    :param str name: A full G2 variable name with 2 or 3 or 4
1823       colons (<p>:<h>:name[:<a1>][:<a2>])
1824
1825    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1826      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1827      the histogram number and the atom number; `name` will always be
1828      a str; and `description` is str or `None`.
1829      If the variable name is incorrectly formed (for example, wrong
1830      number of colons), `None` is returned instead of a list.
1831    '''
1832    l = varname.split(':')
1833    if len(l) == 2:     #SASD parameter name
1834        return varname,l[0],getDescr(l[1])
1835    if len(l) == 3:
1836        l += [None,None]
1837    elif len(l) == 4:
1838        l += [None]
1839    elif len(l) != 5:
1840        return None
1841    for i in (0,1,3,4):
1842        if l[i] == "":
1843            l[i] = None
1844    l += [getDescr(l[2])]
1845    return l
1846
1847def CompileVarDesc():
1848    '''Set the values in the variable lookup tables
1849    (:attr:`reVarDesc` and :attr:`reVarStep`).
1850    This is called in :func:`getDescr` and :func:`getVarStep` so this
1851    initialization is always done before use.
1852
1853    Note that keys may contain regular expressions, where '[xyz]'
1854    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range
1855    of values). '.*' matches any string. For example::
1856
1857    'AUiso':'Atomic isotropic displacement parameter',
1858
1859    will match variable ``'p::AUiso:a'``.
1860    If parentheses are used in the key, the contents of those parentheses can be
1861    used in the value, such as::
1862
1863    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1864
1865    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1866    in the value when used.
1867
1868    '''
1869    if reVarDesc: return # already done
1870    for key,value in {
1871        # derived or other sequential vars
1872        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1873        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1874        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1875        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1876        # ambiguous, alas:
1877        'Scale' : 'Phase or Histogram scale factor',
1878        # Phase vars (p::<var>)
1879        'A([0-5])' : ('Reciprocal metric tensor component \\1',1e-5),
1880        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1881        # Atom vars (p::<var>:a)
1882        'dA([xyz])$' : ('change to atomic coordinate, \\1',1e-6),
1883        'A([xyz])$' : '\\1 fractional atomic coordinate',
1884        'AUiso':('Atomic isotropic displacement parameter',1e-4),
1885        'AU([123][123])':('Atomic anisotropic displacement parameter U\\1',1e-4),
1886        'Afrac': ('Atomic site fraction parameter',1e-5),
1887        'Amul': 'Atomic site multiplicity value',
1888        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1889        # Hist (:h:<var>) & Phase (HAP) vars (p:h:<var>)
1890        'Back': 'Background term',
1891        'BkPkint;(.*)':'Background peak #\\1 intensity',
1892        'BkPkpos;(.*)':'Background peak #\\1 position',
1893        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1894        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1895#        'Back File' : 'Background file name',
1896        'BF mult' : 'Background file multiplier',
1897        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1898        'D([123][123])' : 'Anisotropic strain coef. \\1',
1899        'Extinction' : 'Extinction coef.',
1900        'MD' : 'March-Dollase coef.',
1901        'Mustrain;.*' : 'Microstrain coef.',
1902        'Size;.*' : 'Crystallite size value',
1903        'eA$' : 'Cubic mustrain value',
1904        'Ep$' : 'Primary extinction',
1905        'Es$' : 'Secondary type II extinction',
1906        'Eg$' : 'Secondary type I extinction',
1907        'Flack' : 'Flack parameter',
1908        'TwinFr' : 'Twin fraction',
1909        'Layer Disp'  : 'Layer displacement along beam',
1910        #Histogram vars (:h:<var>)
1911        'Absorption' : 'Absorption coef.',
1912        'Displace([XY])' : ('Debye-Scherrer sample displacement \\1',0.1),
1913        'Lam' : ('Wavelength',1e-6),
1914        'I\\(L2\\)\\/I\\(L1\\)' : ('Ka2/Ka1 intensity ratio',0.001),
1915        'Polariz\\.' : ('Polarization correction',1e-3),
1916        'SH/L' : ('FCJ peak asymmetry correction',1e-4),
1917        '([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),
1918        '([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),
1919        'Zero' : 'Debye-Scherrer zero correction',
1920        'Shift' : 'Bragg-Brentano sample displ.',
1921        'SurfRoughA' : 'Bragg-Brenano surface roughness A',
1922        'SurfRoughB' : 'Bragg-Brenano surface roughness B',
1923        'Transparency' : 'Bragg-Brentano sample tranparency',
1924        'DebyeA' : 'Debye model amplitude',
1925        'DebyeR' : 'Debye model radius',
1926        'DebyeU' : 'Debye model Uiso',
1927        'RBV.*' : 'Vector rigid body parameter',
1928        'RBRO([aijk])' : 'Residue rigid body orientation parameter \\1',
1929        'RBRP([xyz])' : 'Residue rigid body \\1 position parameter',
1930        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1931        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1932        'RBRU' : 'Residue rigid body group Uiso param.',
1933        'constr([0-9]*)' : 'Parameter from constraint',
1934        'nv-([^_]+)_*' : 'New variable constraint parameter named \\1',
1935        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1936        'mV([0-2])$' : 'Modulation vector component \\1',
1937        'Fsin'  :   'Sin site fraction modulation',
1938        'Fcos'  :   'Cos site fraction modulation',
1939        'Fzero'  :   'Crenel function offset',      #may go away
1940        'Fwid'   :   'Crenel function width',
1941        'Tmin'   :   'ZigZag/Block min location',
1942        'Tmax'   :   'ZigZag/Block max location',
1943        '([XYZ])max': 'ZigZag/Block max value for \\1',
1944        '([XYZ])sin'  : 'Sin position wave for \\1',
1945        '([XYZ])cos'  : 'Cos position wave for \\1',
1946        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1947        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1948        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1949        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1950        # PDF peak parms (l:<var>;l = peak no.)
1951        'PDFpos'  : 'PDF peak position',
1952        'PDFmag'  : 'PDF peak magnitude',
1953        'PDFsig'  : 'PDF peak std. dev.',
1954        # SASD vars (l:<var>;l = component)
1955        'Aspect ratio' : 'Particle aspect ratio',
1956        'Length' : 'Cylinder length',
1957        'Diameter' : 'Cylinder/disk diameter',
1958        'Thickness' : 'Disk thickness',
1959        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1960        'Dist' : 'Interparticle distance',
1961        'VolFr' : 'Dense scatterer volume fraction',
1962        'epis' : 'Sticky sphere epsilon',
1963        'Sticky' : 'Stickyness',
1964        'Depth' : 'Well depth',
1965        'Width' : 'Well width',
1966        'Volume' : 'Particle volume',
1967        'Radius' : 'Sphere/cylinder/disk radius',
1968        'Mean' : 'Particle mean radius',
1969        'StdDev' : 'Standard deviation in Mean',
1970        'G$': 'Guinier prefactor',
1971        'Rg$': 'Guinier radius of gyration',
1972        'B$': 'Porod prefactor',
1973        'P$': 'Porod power',
1974        'Cutoff': 'Porod cutoff',
1975        'PkInt': 'Bragg peak intensity',
1976        'PkPos': 'Bragg peak position',
1977        'PkSig': 'Bragg peak sigma',
1978        'PkGam': 'Bragg peak gamma',
1979        'e([12][12])' : 'strain tensor e\\1',   # strain vars e11, e22, e12
1980        'Dcalc': 'Calc. d-spacing',
1981        'Back$': 'background parameter',
1982        'pos$': 'peak position',
1983        'int$': 'peak intensity',
1984        'WgtFrac':'phase weight fraction',
1985        'alpha':'TOF profile term',
1986        'alpha-[01]':'Pink profile term',
1987        'beta-[01q]':'TOF/Pink profile term',
1988        'sig-[012q]':'TOF profile term',
1989        'dif[ABC]':'TOF to d-space calibration',
1990        'C\\([0-9]*,[0-9]*\\)' : 'spherical harmonics preferred orientation coef.',
1991        'Pressure': 'Pressure level for measurement in MPa',
1992        'Temperature': 'T value for measurement, K',
1993        'FreePrm([123])': 'User defined measurement parameter \\1',
1994        'Gonio. radius': 'Distance from sample to detector, mm',
1995        }.items():
1996        # Needs documentation: HAP: LayerDisp, LeBail, newLeBail
1997        # hist: Azimuth, Chi, Omega, Phi, Bank, nDebye, nPeaks
1998       
1999        if len(value) == 2:
2000            #VarDesc[key] = value[0]
2001            reVarDesc[re.compile(key)] = value[0]
2002            reVarStep[re.compile(key)] = value[1]
2003        else:
2004            #VarDesc[key] = value
2005            reVarDesc[re.compile(key)] = value
2006
2007def removeNonRefined(parmList):
2008    '''Remove items from variable list that are not refined and should not
2009    appear as options for constraints
2010
2011    :param list parmList: a list of strings of form "p:h:VAR:a" where
2012      VAR is the variable name
2013
2014    :returns: a list after removing variables where VAR matches a
2015      entry in local variable NonRefinedList
2016    '''
2017    NonRefinedList = ['Omega','Type','Chi','Phi', 'Azimuth','Gonio. radius',
2018                          'Lam1','Lam2','Back','Temperature','Pressure',
2019                          'FreePrm1','FreePrm2','FreePrm3',
2020                          'Source','nPeaks','LeBail','newLeBail','Bank',
2021                          'nDebye', #'',
2022                    ]
2023    return [prm for prm in parmList if prm.split(':')[2] not in NonRefinedList]
2024       
2025def getDescr(name):
2026    '''Return a short description for a GSAS-II variable
2027
2028    :param str name: The descriptive part of the variable name without colons (:)
2029
2030    :returns: a short description or None if not found
2031    '''
2032
2033    CompileVarDesc() # compile the regular expressions, if needed
2034    for key in reVarDesc:
2035        m = key.match(name)
2036        if m:
2037            reVarDesc[key]
2038            return m.expand(reVarDesc[key])
2039    return None
2040
2041def getVarStep(name,parmDict=None):
2042    '''Return a step size for computing the derivative of a GSAS-II variable
2043
2044    :param str name: A complete variable name (with colons, :)
2045    :param dict parmDict: A dict with parameter values or None (default)
2046
2047    :returns: a float that should be an appropriate step size, either from
2048      the value supplied in :func:`CompileVarDesc` or based on the value for
2049      name in parmDict, if supplied. If not found or the value is zero,
2050      a default value of 1e-5 is used. If parmDict is None (default) and
2051      no value is provided in :func:`CompileVarDesc`, then None is returned.
2052    '''
2053    CompileVarDesc() # compile the regular expressions, if needed
2054    for key in reVarStep:
2055        m = key.match(name)
2056        if m:
2057            return reVarStep[key]
2058    if parmDict is None: return None
2059    val = parmDict.get(key,0.0)
2060    if abs(val) > 0.05:
2061        return abs(val)/1000.
2062    else:
2063        return 1e-5
2064
2065def GenWildCard(varlist):
2066    '''Generate wildcard versions of G2 variables. These introduce '*'
2067    for a phase, histogram or atom number (but only for one of these
2068    fields) but only when there is more than one matching variable in the
2069    input variable list. So if the input is this::
2070
2071      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
2072
2073    then the output will be this::
2074
2075       wildList = ['*::AUiso:0', '0::AUiso:*']
2076
2077    :param list varlist: an input list of GSAS-II variable names
2078      (such as 0::AUiso:0)
2079
2080    :returns: wildList, the generated list of wild card variable names.
2081    '''
2082    wild = []
2083    for i in (0,1,3):
2084        currentL = varlist[:]
2085        while currentL:
2086            item1 = currentL.pop(0)
2087            i1splt = item1.split(':')
2088            if i >= len(i1splt): continue
2089            if i1splt[i]:
2090                nextL = []
2091                i1splt[i] = '[0-9]+'
2092                rexp = re.compile(':'.join(i1splt))
2093                matchlist = [item1]
2094                for nxtitem in currentL:
2095                    if rexp.match(nxtitem):
2096                        matchlist += [nxtitem]
2097                    else:
2098                        nextL.append(nxtitem)
2099                if len(matchlist) > 1:
2100                    i1splt[i] = '*'
2101                    wild.append(':'.join(i1splt))
2102                currentL = nextL
2103    return wild
2104
2105def LookupWildCard(varname,varlist):
2106    '''returns a list of variable names from list varname
2107    that match wildcard name in varname
2108
2109    :param str varname: a G2 variable name containing a wildcard
2110      (such as \\*::var)
2111    :param list varlist: the list of all variable names used in
2112      the current project
2113    :returns: a list of matching GSAS-II variables (may be empty)
2114    '''
2115    rexp = re.compile(varname.replace('*','[0-9]+'))
2116    return sorted([var for var in varlist if rexp.match(var)])
2117
2118def prmLookup(name,prmDict):
2119    '''Looks for a parameter in a min/max dictionary, optionally
2120    considering a wild card for histogram or atom number (use of
2121    both will never occur at the same time).
2122
2123    :param name: a GSAS-II parameter name (str, see :func:`getVarDescr`
2124      and :func:`CompileVarDesc`) or a :class:`G2VarObj` object.
2125    :param dict prmDict: a min/max dictionary, (parmMinDict
2126      or parmMaxDict in Controls) where keys are :class:`G2VarObj`
2127      objects.
2128    :returns: Two values, (**matchname**, **value**), are returned where:
2129
2130       * **matchname** *(str)* is the :class:`G2VarObj` object
2131         corresponding to the actual matched name,
2132         which could contain a wildcard even if **name** does not; and
2133       * **value** *(float)* which contains the parameter limit.
2134    '''
2135    for key,value in prmDict.items():
2136        if str(key) == str(name): return key,value
2137        if key == name: return key,value
2138    return None,None
2139       
2140
2141def _lookup(dic,key):
2142    '''Lookup a key in a dictionary, where None returns an empty string
2143    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
2144    '''
2145    if key is None:
2146        return ""
2147    elif key == "*":
2148        return "*"
2149    else:
2150        return dic.get(key,'?')
2151
2152def SortVariables(varlist):
2153    '''Sorts variable names in a sensible manner
2154    '''
2155    def cvnnums(var):
2156        v = []
2157        for i in var.split(':'):
2158            if i == '':
2159                v.append(-1)
2160                continue
2161            try:
2162                v.append(int(i))
2163            except:
2164                v.append(i)
2165        return v
2166    return sorted(varlist,key=cvnnums)
2167
2168class G2VarObj(object):
2169    '''Defines a GSAS-II variable either using the phase/atom/histogram
2170    unique Id numbers or using a character string that specifies
2171    variables by phase/atom/histogram number (which can change).
2172    Note that :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`,
2173    which calls :func:`IndexAllIds` (or
2174    :func:`GSASIIscriptable.G2Project.index_ids`) should be used to
2175    (re)load the current Ids
2176    before creating or later using the G2VarObj object.
2177
2178    This can store rigid body variables, but does not translate the residue # and
2179    body # to/from random Ids
2180
2181    A :class:`G2VarObj` object can be created with a single parameter:
2182
2183    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
2184      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
2185
2186     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
2187     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
2188     * a is the atom number (which may be left blank in which case the third colon is omitted).
2189       The atom number can be specified as '*' if a phase number is specified (not as '*').
2190       For rigid body variables, specify a will be a string of form "residue:body#"
2191
2192      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
2193      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
2194      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
2195      For a rigid body variables, AtomID is a string of form "residue:body#".
2196
2197    If four positional arguments are supplied, they are:
2198
2199    :param str/int phasenum: The number for the phase (or None or '*')
2200    :param str/int histnum: The number for the histogram (or None or '*')
2201    :param str varname: a single value can be used to create a :class:`G2VarObj`
2202    :param str/int atomnum: The number for the atom (or None or '*')
2203
2204    '''
2205    IDdict = {}
2206    IDdict['phases'] = {}
2207    IDdict['hists'] = {}
2208    IDdict['atoms'] = {}
2209    def __init__(self,*args):
2210        self.phase = None
2211        self.histogram = None
2212        self.name = ''
2213        self.atom = None
2214        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
2215            # single arg with 4 values
2216            self.phase,self.histogram,self.name,self.atom = args[0]
2217        elif len(args) == 1 and ':' in args[0]:
2218            #parse a string
2219            lst = args[0].split(':')
2220            if lst[0] == '*':
2221                self.phase = '*'
2222                if len(lst) > 3:
2223                    self.atom = lst[3]
2224                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2225            elif lst[1] == '*':
2226                self.histogram = '*'
2227                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2228            else:
2229                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
2230                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
2231                if len(lst) == 4:
2232                    if lst[3] == '*':
2233                        self.atom = '*'
2234                    else:
2235                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
2236                elif len(lst) == 5:
2237                    self.atom = lst[3]+":"+lst[4]
2238                elif len(lst) == 3:
2239                    pass
2240                else:
2241                    raise Exception("Too many colons in var name "+str(args[0]))
2242            self.name = lst[2]
2243        elif len(args) == 4:
2244            if args[0] == '*':
2245                self.phase = '*'
2246                self.atom = args[3]
2247            else:
2248                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
2249                if args[3] == '*':
2250                    self.atom = '*'
2251                elif args[0] is not None:
2252                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
2253            if args[1] == '*':
2254                self.histogram = '*'
2255            else:
2256                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
2257            self.name = args[2]
2258        else:
2259            raise Exception("Incorrectly called GSAS-II parameter name")
2260
2261        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
2262
2263    def __str__(self):
2264        return self.varname()
2265
2266    def __hash__(self):
2267        'Allow G2VarObj to be a dict key by implementing hashing'
2268        return hash(self.varname())
2269
2270    def varname(self):
2271        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
2272        string (p:h:<var>:a) or (p:h:<var>)
2273
2274        :returns: the variable name as a str
2275        '''
2276        a = ""
2277        if self.phase == "*":
2278            ph = "*"
2279            if self.atom:
2280                a = ":" + str(self.atom)
2281        else:
2282            ph = _lookup(PhaseRanIdLookup,self.phase)
2283            if self.atom == '*':
2284                a = ':*'
2285            elif self.atom:
2286                if ":" in str(self.atom):
2287                    a = ":" + str(self.atom)
2288                elif ph in AtomRanIdLookup:
2289                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
2290                else:
2291                    a = ":?"
2292        if self.histogram == "*":
2293            hist = "*"
2294        else:
2295            hist = _lookup(HistRanIdLookup,self.histogram)
2296        s = (ph + ":" + hist + ":" + str(self.name)) + a
2297        return s
2298
2299    def __repr__(self):
2300        '''Return the detailed contents of the object
2301        '''
2302        s = "<"
2303        if self.phase == '*':
2304            s += "Phases: all; "
2305            if self.atom is not None:
2306                if ":" in str(self.atom):
2307                    s += "Rigid body" + str(self.atom) + "; "
2308                else:
2309                    s += "Atom #" + str(self.atom) + "; "
2310        elif self.phase is not None:
2311            ph =  _lookup(PhaseRanIdLookup,self.phase)
2312            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
2313            if self.atom == '*':
2314                s += "Atoms: all; "
2315            elif ":" in str(self.atom):
2316                s += "Rigid body" + str(self.atom) + "; "
2317            elif self.atom is not None:
2318                s += "Atom rId=" + str(self.atom)
2319                if ph in AtomRanIdLookup:
2320                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
2321                else:
2322                    s += " (#? -- not found!); "
2323        if self.histogram == '*':
2324            s += "Histograms: all; "
2325        elif self.histogram is not None:
2326            hist = _lookup(HistRanIdLookup,self.histogram)
2327            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
2328        s += 'Variable name="' + str(self.name) + '">'
2329        return s+" ("+self.varname()+")"
2330
2331    def __eq__(self, other):
2332        '''Allow comparison of G2VarObj to other G2VarObj objects or strings.
2333        If any field is a wildcard ('*') that field matches.
2334        '''
2335        if type(other) is str:
2336            other = G2VarObj(other)
2337        elif type(other) is not G2VarObj:
2338            raise Exception("Invalid type ({}) for G2VarObj comparison with {}"
2339                            .format(type(other),other))
2340        if self.phase != other.phase and self.phase != '*' and other.phase != '*':
2341            return False
2342        if self.histogram != other.histogram and self.histogram != '*' and other.histogram != '*':
2343            return False
2344        if self.atom != other.atom and self.atom != '*' and other.atom != '*':
2345            return False
2346        if self.name != other.name:
2347            return False
2348        return True
2349
2350    def _show(self):
2351        'For testing, shows the current lookup table'
2352        print ('phases'+ self.IDdict['phases'])
2353        print ('hists'+ self.IDdict['hists'])
2354        print ('atomDict'+ self.IDdict['atoms'])
2355
2356#==========================================================================
2357def SetDefaultSample():
2358    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
2359    return {
2360        'InstrName':'',
2361        'ranId':ran.randint(0,sys.maxsize),
2362        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
2363        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],
2364        'Temperature':300.,'Pressure':0.1,'Time':0.0,
2365        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
2366        'Gonio. radius':200.0,
2367        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
2368#SASD items
2369        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
2370        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
2371        'Trans':1.0,                            #measured transmission
2372        'SlitLen':0.0,                          #Slit length - in Q(A-1)
2373        }
2374######################################################################
2375class ImportBaseclass(object):
2376    '''Defines a base class for the reading of input files (diffraction
2377    data, coordinates,...). See :ref:`Writing a Import Routine<import_routines>`
2378    for an explanation on how to use a subclass of this class.
2379    '''
2380    class ImportException(Exception):
2381        '''Defines an Exception that is used when an import routine hits an expected error,
2382        usually in .Reader.
2383
2384        Good practice is that the Reader should define a value in self.errors that
2385        tells the user some information about what is wrong with their file.
2386        '''
2387        pass
2388
2389    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
2390    def __init__(self,formatName,longFormatName=None,
2391                 extensionlist=[],strictExtension=False,):
2392        self.formatName = formatName # short string naming file type
2393        if longFormatName: # longer string naming file type
2394            self.longFormatName = longFormatName
2395        else:
2396            self.longFormatName = formatName
2397        # define extensions that are allowed for the file type
2398        # for windows, remove any extensions that are duplicate, as case is ignored
2399        if sys.platform == 'windows' and extensionlist:
2400            extensionlist = list(set([s.lower() for s in extensionlist]))
2401        self.extensionlist = extensionlist
2402        # If strictExtension is True, the file will not be read, unless
2403        # the extension matches one in the extensionlist
2404        self.strictExtension = strictExtension
2405        self.errors = ''
2406        self.warnings = ''
2407        self.SciPy = False          #image reader needed scipy
2408        # used for readers that will use multiple passes to read
2409        # more than one data block
2410        self.repeat = False
2411        self.selections = []
2412        self.repeatcount = 0
2413        self.readfilename = '?'
2414        self.scriptable = False
2415        #print 'created',self.__class__
2416
2417    def ReInitialize(self):
2418        'Reinitialize the Reader to initial settings'
2419        self.errors = ''
2420        self.warnings = ''
2421        self.SciPy = False          #image reader needed scipy
2422        self.repeat = False
2423        self.repeatcount = 0
2424        self.readfilename = '?'
2425
2426
2427#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
2428#        '''This method must be supplied in the child class to read the file.
2429#        if the read fails either return False or raise an Exception
2430#        preferably of type ImportException.
2431#        '''
2432#        #start reading
2433#        raise ImportException("Error occurred while...")
2434#        self.errors += "Hint for user on why the error occur
2435#        return False # if an error occurs
2436#        return True # if read OK
2437
2438    def ExtensionValidator(self, filename):
2439        '''This methods checks if the file has the correct extension
2440       
2441        :returns:
2442       
2443          * False if this filename will not be supported by this reader (only
2444            when strictExtension is True)
2445          * True if the extension matches the list supplied by the reader
2446          * None if the reader allows un-registered extensions
2447         
2448        '''
2449        if filename:
2450            ext = ospath.splitext(filename)[1]
2451            if not ext and self.strictExtension: return False
2452            for ext in self.extensionlist:               
2453                if sys.platform == 'windows':
2454                    if filename.lower().endswith(ext): return True
2455                else:
2456                    if filename.endswith(ext): return True
2457        if self.strictExtension:
2458            return False
2459        else:
2460            return None
2461
2462    def ContentsValidator(self, filename):
2463        '''This routine will attempt to determine if the file can be read
2464        with the current format.
2465        This will typically be overridden with a method that
2466        takes a quick scan of [some of]
2467        the file contents to do a "sanity" check if the file
2468        appears to match the selected format.
2469        the file must be opened here with the correct format (binary/text)
2470        '''
2471        #filepointer.seek(0) # rewind the file pointer
2472        return True
2473
2474    def CIFValidator(self, filepointer):
2475        '''A :meth:`ContentsValidator` for use to validate CIF files.
2476        '''
2477        filepointer.seek(0)
2478        for i,l in enumerate(filepointer):
2479            if i >= 1000: return True
2480            '''Encountered only blank lines or comments in first 1000
2481            lines. This is unlikely, but assume it is CIF anyway, since we are
2482            even less likely to find a file with nothing but hashes and
2483            blank lines'''
2484            line = l.strip()
2485            if len(line) == 0: # ignore blank lines
2486                continue
2487            elif line.startswith('#'): # ignore comments
2488                continue
2489            elif line.startswith('data_'): # on the right track, accept this file
2490                return True
2491            else: # found something invalid
2492                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
2493                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
2494                    self.errors += '  '+str(l)
2495                else:
2496                    self.errors += '  (binary)'
2497                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
2498                self.errors += '\n        a data_ statement begins a block.'
2499                return False
2500
2501######################################################################
2502class ImportPhase(ImportBaseclass):
2503    '''Defines a base class for the reading of files with coordinates
2504
2505    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
2506    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase` and in
2507    :func:`GSASIIscriptable.import_generic`.
2508    See :ref:`Writing a Import Routine<import_routines>`
2509    for an explanation on how to use this class.
2510
2511    '''
2512    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2513        strictExtension=False,):
2514        # call parent __init__
2515        ImportBaseclass.__init__(self,formatName,longFormatName,
2516            extensionlist,strictExtension)
2517        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
2518        self.SymOps = {} # specified when symmetry ops are in file (e.g. CIF)
2519        self.Constraints = None
2520
2521######################################################################
2522class ImportStructFactor(ImportBaseclass):
2523    '''Defines a base class for the reading of files with tables
2524    of structure factors.
2525
2526    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
2527    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
2528    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2529    :meth:`Reader`.
2530
2531    See :ref:`Writing a Import Routine<import_routines>`
2532    for an explanation on how to use import classes in general. The specifics
2533    for reading a structure factor histogram require that
2534    the ``Reader()`` routine in the import
2535    class need to do only a few things: It
2536    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2537    and set :attr:`Parameters` with the instrument parameters
2538    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2539    '''
2540    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2541        strictExtension=False,):
2542        ImportBaseclass.__init__(self,formatName,longFormatName,
2543            extensionlist,strictExtension)
2544
2545        # define contents of Structure Factor entry
2546        self.Parameters = []
2547        'self.Parameters is a list with two dicts for data parameter settings'
2548        self.InitParameters()
2549        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2550        self.Banks = []             #for multi bank data (usually TOF)
2551        '''self.RefDict is a dict containing the reflection information, as read from the file.
2552        Item 'RefList' contains the reflection information. See the
2553        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
2554        for the contents of each row. Dict element 'FF'
2555        contains the form factor values for each element type; if this entry
2556        is left as initialized (an empty list) it will be initialized as needed later.
2557        '''
2558    def ReInitialize(self):
2559        'Reinitialize the Reader to initial settings'
2560        ImportBaseclass.ReInitialize(self)
2561        self.InitParameters()
2562        self.Banks = []             #for multi bank data (usually TOF)
2563        self.RefDict = {'RefList':[],'FF':{},'Super':0}
2564
2565    def InitParameters(self):
2566        'initialize the instrument parameters structure'
2567        Lambda = 0.70926
2568        HistType = 'SXC'
2569        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2570                            'Lam':[Lambda,Lambda]
2571                            }, {}]
2572        'Parameters is a list with two dicts for data parameter settings'
2573
2574    def UpdateParameters(self,Type=None,Wave=None):
2575        'Revise the instrument parameters'
2576        if Type is not None:
2577            self.Parameters[0]['Type'] = [Type,Type]
2578        if Wave is not None:
2579            self.Parameters[0]['Lam'] = [Wave,Wave]
2580
2581######################################################################
2582class ImportPowderData(ImportBaseclass):
2583    '''Defines a base class for the reading of files with powder data.
2584
2585    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2586    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder` and in
2587    :func:`GSASIIscriptable.import_generic`.
2588    See :ref:`Writing a Import Routine<import_routines>`
2589    for an explanation on how to use this class.
2590    '''
2591    def __init__(self,formatName,longFormatName=None,
2592        extensionlist=[],strictExtension=False,):
2593        ImportBaseclass.__init__(self,formatName,longFormatName,
2594            extensionlist,strictExtension)
2595        self.clockWd = None  # used in TOF
2596        self.ReInitialize()
2597
2598    def ReInitialize(self):
2599        'Reinitialize the Reader to initial settings'
2600        ImportBaseclass.ReInitialize(self)
2601        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2602        self.powderdata = [] # Powder dataset
2603        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2604                np.array(x), # x-axis values
2605                np.array(y), # powder pattern intensities
2606                np.array(w), # 1/sig(intensity)^2 values (weights)
2607                np.array(yc), # calc. intensities (zero)
2608                np.array(yb), # calc. background (zero)
2609                np.array(yd), # obs-calc profiles
2610        '''
2611        self.comments = []
2612        self.idstring = ''
2613        self.Sample = SetDefaultSample() # default sample parameters
2614        self.Controls = {}  # items to be placed in top-level Controls
2615        self.GSAS = None     # used in TOF
2616        self.repeat_instparm = True # Should a parm file be
2617        #                             used for multiple histograms?
2618        self.instparm = None # name hint from file of instparm to use
2619        self.instfile = '' # full path name to instrument parameter file
2620        self.instbank = '' # inst parm bank number
2621        self.instmsg = ''  # a label that gets printed to show
2622                           # where instrument parameters are from
2623        self.numbanks = 1
2624        self.instdict = {} # place items here that will be transferred to the instrument parameters
2625        self.pwdparms = {} # place parameters that are transferred directly to the tree
2626                           # here (typically from an existing GPX file)
2627######################################################################
2628class ImportSmallAngleData(ImportBaseclass):
2629    '''Defines a base class for the reading of files with small angle data.
2630    See :ref:`Writing a Import Routine<import_routines>`
2631    for an explanation on how to use this class.
2632    '''
2633    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2634        strictExtension=False,):
2635
2636        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2637            strictExtension)
2638        self.ReInitialize()
2639
2640    def ReInitialize(self):
2641        'Reinitialize the Reader to initial settings'
2642        ImportBaseclass.ReInitialize(self)
2643        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2644        self.smallangledata = [] # SASD dataset
2645        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2646                np.array(x), # x-axis values
2647                np.array(y), # powder pattern intensities
2648                np.array(w), # 1/sig(intensity)^2 values (weights)
2649                np.array(yc), # calc. intensities (zero)
2650                np.array(yd), # obs-calc profiles
2651                np.array(yb), # preset bkg
2652        '''
2653        self.comments = []
2654        self.idstring = ''
2655        self.Sample = SetDefaultSample()
2656        self.GSAS = None     # used in TOF
2657        self.clockWd = None  # used in TOF
2658        self.numbanks = 1
2659        self.instdict = {} # place items here that will be transferred to the instrument parameters
2660
2661######################################################################
2662class ImportReflectometryData(ImportBaseclass):
2663    '''Defines a base class for the reading of files with reflectometry data.
2664    See :ref:`Writing a Import Routine<import_routines>`
2665    for an explanation on how to use this class.
2666    '''
2667    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2668        strictExtension=False,):
2669
2670        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2671            strictExtension)
2672        self.ReInitialize()
2673
2674    def ReInitialize(self):
2675        'Reinitialize the Reader to initial settings'
2676        ImportBaseclass.ReInitialize(self)
2677        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2678        self.reflectometrydata = [] # SASD dataset
2679        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2680                np.array(x), # x-axis values
2681                np.array(y), # powder pattern intensities
2682                np.array(w), # 1/sig(intensity)^2 values (weights)
2683                np.array(yc), # calc. intensities (zero)
2684                np.array(yd), # obs-calc profiles
2685                np.array(yb), # preset bkg
2686        '''
2687        self.comments = []
2688        self.idstring = ''
2689        self.Sample = SetDefaultSample()
2690        self.GSAS = None     # used in TOF
2691        self.clockWd = None  # used in TOF
2692        self.numbanks = 1
2693        self.instdict = {} # place items here that will be transferred to the instrument parameters
2694
2695######################################################################
2696class ImportPDFData(ImportBaseclass):
2697    '''Defines a base class for the reading of files with PDF G(R) data.
2698    See :ref:`Writing a Import Routine<import_routines>`
2699    for an explanation on how to use this class.
2700    '''
2701    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2702        strictExtension=False,):
2703
2704        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2705            strictExtension)
2706        self.ReInitialize()
2707
2708    def ReInitialize(self):
2709        'Reinitialize the Reader to initial settings'
2710        ImportBaseclass.ReInitialize(self)
2711        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2712        self.pdfdata = [] # PDF G(R) dataset
2713        '''A pdf g(r) data set is a list with items [x,y]:
2714                np.array(x), # r-axis values
2715                np.array(y), # pdf g(r)
2716        '''
2717        self.comments = []
2718        self.idstring = ''
2719        self.numbanks = 1
2720
2721######################################################################
2722class ImportImage(ImportBaseclass):
2723    '''Defines a base class for the reading of images
2724
2725    Images are read in only these places:
2726
2727      * Initial reading is typically done from a menu item
2728        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2729        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2730        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2731        :meth:`Reader`. This returns a list of reader objects for each read image.
2732        Also used in :func:`GSASIIscriptable.import_generic`.
2733
2734      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2735        directly into the data tree.
2736
2737      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2738
2739    When reading an image, the ``Reader()`` routine in the ImportImage class
2740    should set:
2741
2742      * :attr:`Comments`: a list of strings (str),
2743      * :attr:`Npix`: the number of pixels in the image (int),
2744      * :attr:`Image`: the actual image as a numpy array (np.array)
2745      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2746        data items are needed:
2747
2748         * 'pixelSize': size of each pixel in microns (such as ``[200.,200.]``.
2749         * 'wavelength': wavelength in :math:`\\AA`.
2750         * 'distance': distance of detector from sample in cm.
2751         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2752         * 'size': size of image (such as ``[2048,2048]``).
2753         * 'ImageTag': image number or other keyword used to retrieve image from
2754           a multi-image data file (defaults to ``1`` if not specified).
2755         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2756
2757    optional data items:
2758
2759      * :attr:`repeat`: set to True if there are additional images to
2760        read in the file, False otherwise
2761      * :attr:`repeatcount`: set to the number of the image.
2762
2763    Note that the above is initialized with :meth:`InitParameters`.
2764    (Also see :ref:`Writing a Import Routine<import_routines>`
2765    for an explanation on how to use import classes in general.)
2766    '''
2767    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2768        strictExtension=False,):
2769        ImportBaseclass.__init__(self,formatName,longFormatName,
2770            extensionlist,strictExtension)
2771        self.InitParameters()
2772
2773    def ReInitialize(self):
2774        'Reinitialize the Reader to initial settings -- not used at present'
2775        ImportBaseclass.ReInitialize(self)
2776        self.InitParameters()
2777
2778    def InitParameters(self):
2779        'initialize the instrument parameters structure'
2780        self.Comments = ['No comments']
2781        self.Data = {}
2782        self.Npix = 0
2783        self.Image = None
2784        self.repeat = False
2785        self.repeatcount = 1
2786        self.sumfile = ''
2787
2788    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2789        '''Optionally, call this after reading in an image to load it into the tree.
2790        This saves time by preventing a reread of the same information.
2791        '''
2792        if ParentFrame:
2793            ParentFrame.ImageZ = self.Image   # store the image for plotting
2794            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2795            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2796
2797#################################################################################################
2798# shortcut routines
2799exp = np.exp
2800sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2801cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2802tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2803sqrt = sq = lambda x: np.sqrt(x)
2804pi = lambda: np.pi
2805
2806def FindFunction(f):
2807    '''Find the object corresponding to function f
2808
2809    :param str f: a function name such as 'numpy.exp'
2810    :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2811      that defines the package location(s) and where pkgobj
2812      defines the object associated with the function.
2813      If the function is not found, pkgobj is None.
2814    '''
2815    df = f.split('.')
2816    pkgdict = {}
2817    # no listed module name, try in current namespace
2818    if len(df) == 1:
2819        try:
2820            fxnobj = eval(f)
2821            return pkgdict,fxnobj
2822        except (AttributeError, NameError):
2823            return None,None
2824
2825    # includes a package, see if package is already imported
2826    pkgnam = '.'.join(df[:-1])
2827    try:
2828        fxnobj = eval(f)
2829        pkgdict[pkgnam] = eval(pkgnam)
2830        return pkgdict,fxnobj
2831    except (AttributeError, NameError):
2832        pass
2833    # package not yet imported, so let's try
2834    if '.' not in sys.path: sys.path.append('.')
2835    pkgnam = '.'.join(df[:-1])
2836    #for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2837    #    if pkgname:
2838    #        pkgname += '.' + pkg
2839    #    else:
2840    #        pkgname = pkg
2841    try:
2842        exec('import '+pkgnam)
2843        pkgdict[pkgnam] = eval(pkgnam)
2844        fxnobj = eval(f)
2845    except Exception as msg:
2846        print('load of '+pkgnam+' failed with error='+str(msg))
2847        return {},None
2848    # can we access the function? I am not exactly sure what
2849    #    I intended this to test originally (BHT)
2850    try:
2851        fxnobj = eval(f,globals(),pkgdict)
2852        return pkgdict,fxnobj
2853    except Exception as msg:
2854        print('call to',f,' failed with error=',str(msg))
2855        return None,None # not found
2856               
2857class ExpressionObj(object):
2858    '''Defines an object with a user-defined expression, to be used for
2859    secondary fits or restraints. Object is created null, but is changed
2860    using :meth:`LoadExpression`. This contains only the minimum
2861    information that needs to be stored to save and load the expression
2862    and how it is mapped to GSAS-II variables.
2863    '''
2864    def __init__(self):
2865        self.expression = ''
2866        'The expression as a text string'
2867        self.assgnVars = {}
2868        '''A dict where keys are label names in the expression mapping to a GSAS-II
2869        variable. The value a G2 variable name.
2870        Note that the G2 variable name may contain a wild-card and correspond to
2871        multiple values.
2872        '''
2873        self.freeVars = {}
2874        '''A dict where keys are label names in the expression mapping to a free
2875        parameter. The value is a list with:
2876
2877         * a name assigned to the parameter
2878         * a value for to the parameter and
2879         * a flag to determine if the variable is refined.
2880        '''
2881        self.depVar = None
2882
2883        self.lastError = ('','')
2884        '''Shows last encountered error in processing expression
2885        (list of 1-3 str values)'''
2886
2887        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2888        self.distance_atoms = None  # to be used for defining atom distances
2889
2890    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2891        '''Load the expression and associated settings into the object. Raises
2892        an exception if the expression is not parsed, if not all functions
2893        are defined or if not all needed parameter labels in the expression
2894        are defined.
2895
2896        This will not test if the variable referenced in these definitions
2897        are actually in the parameter dictionary. This is checked when the
2898        computation for the expression is done in :meth:`SetupCalc`.
2899
2900        :param str expr: the expression
2901        :param list exprVarLst: parameter labels found in the expression
2902        :param dict varSelect: this will be 0 for Free parameters
2903          and non-zero for expression labels linked to G2 variables.
2904        :param dict varName: Defines a name (str) associated with each free parameter
2905        :param dict varValue: Defines a value (float) associated with each free parameter
2906        :param dict varRefflag: Defines a refinement flag (bool)
2907          associated with each free parameter
2908        '''
2909        self.expression = expr
2910        self.compiledExpr = None
2911        self.freeVars = {}
2912        self.assgnVars = {}
2913        for v in exprVarLst:
2914            if varSelect[v] == 0:
2915                self.freeVars[v] = [
2916                    varName.get(v),
2917                    varValue.get(v),
2918                    varRefflag.get(v),
2919                    ]
2920            else:
2921                self.assgnVars[v] = varName[v]
2922        self.CheckVars()
2923
2924    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2925        '''Load the expression and associated settings from the object into
2926        arrays used for editing.
2927
2928        :param list exprVarLst: parameter labels found in the expression
2929        :param dict varSelect: this will be 0 for Free parameters
2930          and non-zero for expression labels linked to G2 variables.
2931        :param dict varName: Defines a name (str) associated with each free parameter
2932        :param dict varValue: Defines a value (float) associated with each free parameter
2933        :param dict varRefflag: Defines a refinement flag (bool)
2934          associated with each free parameter
2935
2936        :returns: the expression as a str
2937        '''
2938        for v in self.freeVars:
2939            varSelect[v] = 0
2940            varName[v] = self.freeVars[v][0]
2941            varValue[v] = self.freeVars[v][1]
2942            varRefflag[v] = self.freeVars[v][2]
2943        for v in self.assgnVars:
2944            varSelect[v] = 1
2945            varName[v] = self.assgnVars[v]
2946        return self.expression
2947
2948    def GetVaried(self):
2949        'Returns the names of the free parameters that will be refined'
2950        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
2951
2952    def GetVariedVarVal(self):
2953        'Returns the names and values of the free parameters that will be refined'
2954        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
2955
2956    def UpdateVariedVars(self,varyList,values):
2957        'Updates values for the free parameters (after a refinement); only updates refined vars'
2958        for v in self.freeVars:
2959            if not self.freeVars[v][2]: continue
2960            if "::"+self.freeVars[v][0] not in varyList: continue
2961            indx = list(varyList).index("::"+self.freeVars[v][0])
2962            self.freeVars[v][1] = values[indx]
2963
2964    def GetIndependentVars(self):
2965        'Returns the names of the required independent parameters used in expression'
2966        return [self.assgnVars[v] for v in self.assgnVars]
2967
2968    def CheckVars(self):
2969        '''Check that the expression can be parsed, all functions are
2970        defined and that input loaded into the object is internally
2971        consistent. If not an Exception is raised.
2972
2973        :returns: a dict with references to packages needed to
2974          find functions referenced in the expression.
2975        '''
2976        ret = self.ParseExpression(self.expression)
2977        if not ret:
2978            raise Exception("Expression parse error")
2979        exprLblList,fxnpkgdict = ret
2980        # check each var used in expression is defined
2981        defined = list(self.assgnVars.keys()) + list(self.freeVars.keys())
2982        notfound = []
2983        for var in exprLblList:
2984            if var not in defined:
2985                notfound.append(var)
2986        if notfound:
2987            msg = 'Not all variables defined'
2988            msg1 = 'The following variables were not defined: '
2989            msg2 = ''
2990            for var in notfound:
2991                if msg: msg += ', '
2992                msg += var
2993            self.lastError = (msg1,'  '+msg2)
2994            raise Exception(msg)
2995        return fxnpkgdict
2996
2997    def ParseExpression(self,expr):
2998        '''Parse an expression and return a dict of called functions and
2999        the variables used in the expression. Returns None in case an error
3000        is encountered. If packages are referenced in functions, they are loaded
3001        and the functions are looked up into the modules global
3002        workspace.
3003
3004        Note that no changes are made to the object other than
3005        saving an error message, so that this can be used for testing prior
3006        to the save.
3007
3008        :returns: a list of used variables
3009        '''
3010        self.lastError = ('','')
3011        import ast
3012        def ASTtransverse(node,fxn=False):
3013            '''Transverse a AST-parsed expresson, compiling a list of variables
3014            referenced in the expression. This routine is used recursively.
3015
3016            :returns: varlist,fxnlist where
3017              varlist is a list of referenced variable names and
3018              fxnlist is a list of used functions
3019            '''
3020            varlist = []
3021            fxnlist = []
3022            if isinstance(node, list):
3023                for b in node:
3024                    v,f = ASTtransverse(b,fxn)
3025                    varlist += v
3026                    fxnlist += f
3027            elif isinstance(node, ast.AST):
3028                for a, b in ast.iter_fields(node):
3029                    if isinstance(b, ast.AST):
3030                        if a == 'func':
3031                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
3032                            continue
3033                        v,f = ASTtransverse(b,fxn)
3034                        varlist += v
3035                        fxnlist += f
3036                    elif isinstance(b, list):
3037                        v,f = ASTtransverse(b,fxn)
3038                        varlist += v
3039                        fxnlist += f
3040                    elif node.__class__.__name__ == "Name":
3041                        varlist += [b]
3042                    elif fxn and node.__class__.__name__ == "Attribute":
3043                        varlist += [b]
3044            return varlist,fxnlist
3045        try:
3046            exprast = ast.parse(expr)
3047        except SyntaxError:
3048            s = ''
3049            import traceback
3050            for i in traceback.format_exc().splitlines()[-3:-1]:
3051                if s: s += "\n"
3052                s += str(i)
3053            self.lastError = ("Error parsing expression:",s)
3054            return
3055        # find the variables & functions
3056        v,f = ASTtransverse(exprast)
3057        varlist = sorted(list(set(v)))
3058        fxnlist = list(set(f))
3059        pkgdict = {}
3060        # check the functions are defined
3061        for fxn in fxnlist:
3062            fxndict,fxnobj = FindFunction(fxn)
3063            if not fxnobj:
3064                self.lastError = ("Error: Invalid function",fxn,
3065                                  "is not defined")
3066                return
3067            if not hasattr(fxnobj,'__call__'):
3068                self.lastError = ("Error: Not a function.",fxn,
3069                                  "cannot be called as a function")
3070                return
3071            pkgdict.update(fxndict)
3072        return varlist,pkgdict
3073
3074    def GetDepVar(self):
3075        'return the dependent variable, or None'
3076        return self.depVar
3077
3078    def SetDepVar(self,var):
3079        'Set the dependent variable, if used'
3080        self.depVar = var
3081#==========================================================================
3082class ExpressionCalcObj(object):
3083    '''An object used to evaluate an expression from a :class:`ExpressionObj`
3084    object.
3085
3086    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
3087      an expression string and mappings for the parameter labels in that object.
3088    '''
3089    def __init__(self,exprObj):
3090        self.eObj = exprObj
3091        'The expression and mappings; a :class:`ExpressionObj` object'
3092        self.compiledExpr = None
3093        'The expression as compiled byte-code'
3094        self.exprDict = {}
3095        '''dict that defines values for labels used in expression and packages
3096        referenced by functions
3097        '''
3098        self.lblLookup = {}
3099        '''Lookup table that specifies the expression label name that is
3100        tied to a particular GSAS-II parameters in the parmDict.
3101        '''
3102        self.fxnpkgdict = {}
3103        '''a dict with references to packages needed to
3104        find functions referenced in the expression.
3105        '''
3106        self.varLookup = {}
3107        '''Lookup table that specifies the GSAS-II variable(s)
3108        indexed by the expression label name. (Used for only for diagnostics
3109        not evaluation of expression.)
3110        '''
3111        self.su = None
3112        '''Standard error evaluation where supplied by the evaluator
3113        '''
3114        # Patch: for old-style expressions with a (now removed step size)
3115        if '2' in platform.python_version_tuple()[0]: 
3116            basestr = basestring
3117        else:
3118            basestr = str
3119        for v in self.eObj.assgnVars:
3120            if not isinstance(self.eObj.assgnVars[v], basestr):
3121                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
3122        self.parmDict = {}
3123        '''A copy of the parameter dictionary, for distance and angle computation
3124        '''
3125
3126    def SetupCalc(self,parmDict):
3127        '''Do all preparations to use the expression for computation.
3128        Adds the free parameter values to the parameter dict (parmDict).
3129        '''
3130        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3131            return
3132        self.fxnpkgdict = self.eObj.CheckVars()
3133        # all is OK, compile the expression
3134        self.compiledExpr = compile(self.eObj.expression,'','eval')
3135
3136        # look at first value in parmDict to determine its type
3137        parmsInList = True
3138        if '2' in platform.python_version_tuple()[0]: 
3139            basestr = basestring
3140        else:
3141            basestr = str
3142        for key in parmDict:
3143            val = parmDict[key]
3144            if isinstance(val, basestr):
3145                parmsInList = False
3146                break
3147            try: # check if values are in lists
3148                val = parmDict[key][0]
3149            except (TypeError,IndexError):
3150                parmsInList = False
3151            break
3152
3153        # set up the dicts needed to speed computations
3154        self.exprDict = {}
3155        self.lblLookup = {}
3156        self.varLookup = {}
3157        for v in self.eObj.freeVars:
3158            varname = self.eObj.freeVars[v][0]
3159            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
3160            self.lblLookup[varname] = v
3161            self.varLookup[v] = varname
3162            if parmsInList:
3163                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
3164            else:
3165                parmDict[varname] = self.eObj.freeVars[v][1]
3166            self.exprDict[v] = self.eObj.freeVars[v][1]
3167        for v in self.eObj.assgnVars:
3168            varname = self.eObj.assgnVars[v]
3169            if varname in parmDict:
3170                self.lblLookup[varname] = v
3171                self.varLookup[v] = varname
3172                if parmsInList:
3173                    self.exprDict[v] = parmDict[varname][0]
3174                else:
3175                    self.exprDict[v] = parmDict[varname]
3176            elif '*' in varname:
3177                varlist = LookupWildCard(varname,list(parmDict.keys()))
3178                if len(varlist) == 0:
3179                    raise Exception("No variables match "+str(v))
3180                for var in varlist:
3181                    self.lblLookup[var] = v
3182                if parmsInList:
3183                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
3184                else:
3185                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
3186                self.varLookup[v] = [var for var in varlist]
3187            else:
3188                self.exprDict[v] = None
3189#                raise Exception,"No value for variable "+str(v)
3190        self.exprDict.update(self.fxnpkgdict)
3191
3192    def UpdateVars(self,varList,valList):
3193        '''Update the dict for the expression with a set of values
3194        :param list varList: a list of variable names
3195        :param list valList: a list of corresponding values
3196        '''
3197        for var,val in zip(varList,valList):
3198            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
3199
3200    def UpdateDict(self,parmDict):
3201        '''Update the dict for the expression with values in a dict
3202        :param dict parmDict: a dict of values, items not in use are ignored
3203        '''
3204        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
3205            self.parmDict = parmDict
3206            return
3207        for var in parmDict:
3208            if var in self.lblLookup:
3209                self.exprDict[self.lblLookup[var]] = parmDict[var]
3210
3211    def EvalExpression(self):
3212        '''Evaluate an expression. Note that the expression
3213        and mapping are taken from the :class:`ExpressionObj` expression object
3214        and the parameter values were specified in :meth:`SetupCalc`.
3215        :returns: a single value for the expression. If parameter
3216        values are arrays (for example, from wild-carded variable names),
3217        the sum of the resulting expression is returned.
3218
3219        For example, if the expression is ``'A*B'``,
3220        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
3221
3222        [0.5, 1, 0.5]
3223
3224        then the result will be ``4.0``.
3225        '''
3226        self.su = None
3227        if self.eObj.expression.startswith('Dist'):
3228#            GSASIIpath.IPyBreak()
3229            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
3230            return dist
3231        elif self.eObj.expression.startswith('Angle'):
3232            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
3233            return angle
3234        if self.compiledExpr is None:
3235            raise Exception("EvalExpression called before SetupCalc")
3236        try:
3237            val = eval(self.compiledExpr,globals(),self.exprDict)
3238        except TypeError:
3239            val = None
3240        if not np.isscalar(val):
3241            val = np.sum(val)
3242        return val
3243
3244class G2Exception(Exception):
3245    'A generic GSAS-II exception class'
3246    def __init__(self,msg):
3247        self.msg = msg
3248    def __str__(self):
3249        return repr(self.msg)
3250
3251class G2RefineCancel(Exception):
3252    'Raised when Cancel is pressed in a refinement dialog'
3253    def __init__(self,msg):
3254        self.msg = msg
3255    def __str__(self):
3256        return repr(self.msg)
3257   
3258def HowDidIgetHere(wherecalledonly=False):
3259    '''Show a traceback with calls that brought us to the current location.
3260    Used for debugging.
3261    '''
3262    import traceback
3263    if wherecalledonly:
3264        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
3265        print(i.strip().rstrip())
3266    else:
3267        print (70*'*')
3268        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
3269        print (70*'*')
3270
3271# Note that this is GUI code and should be moved at somepoint
3272def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
3273    '''Create and initialize a new set of PDF tree entries
3274
3275    :param Frame G2frame: main GSAS-II tree frame object
3276    :param str PWDRtree: name of PWDR to be used to create PDF item
3277    :param dict ElList: data structure with composition
3278    :param list Qlimits: Q limits to be used for computing the PDF
3279    :param float numAtm: no. atom in chemical formula
3280    :param float FltBkg: flat background value
3281    :param list PDFnames: previously used PDF names
3282
3283    :returns: the Id of the newly created PDF entry
3284    '''
3285    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
3286    if PDFname in PDFnames:
3287        print('Skipping, entry already exists: '+PDFname)
3288        return None
3289    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
3290    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
3291    Data = {
3292        'Sample':{'Name':PWDRtree,'Mult':1.0},
3293        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
3294        'Container':{'Name':'','Mult':-1.0,'Refine':False},
3295        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
3296        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
3297        'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
3298        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,'Rmin':1.0,
3299        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
3300    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
3301    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
3302        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
3303    return Id
3304#%%
3305class ShowTiming(object):
3306    '''An object to use for timing repeated sections of code.
3307
3308    Create the object with::
3309       tim0 = ShowTiming()
3310
3311    Tag sections of code to be timed with::
3312       tim0.start('start')
3313       tim0.start('in section 1')
3314       tim0.start('in section 2')
3315       
3316    etc. (Note that each section should have a unique label.)
3317
3318    After the last section, end timing with::
3319       tim0.end()
3320
3321    Show timing results with::
3322       tim0.show()
3323       
3324    '''
3325    def __init__(self):
3326        self.timeSum =  []
3327        self.timeStart = []
3328        self.label = []
3329        self.prev = None
3330    def start(self,label):
3331        import time
3332        if label in self.label:
3333            i = self.label.index(label)
3334            self.timeStart[i] = time.time()
3335        else:
3336            i = len(self.label)
3337            self.timeSum.append(0.0)
3338            self.timeStart.append(time.time())
3339            self.label.append(label)
3340        if self.prev is not None:
3341            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
3342        self.prev = i
3343    def end(self):
3344        import time
3345        if self.prev is not None:
3346            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
3347        self.prev = None
3348    def show(self):
3349        sumT = sum(self.timeSum)
3350        print('Timing results (total={:.2f} sec)'.format(sumT))
3351        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
3352            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
3353#%%
3354
3355def validateAtomDrawType(typ,generalData={}):
3356    '''Confirm that the selected Atom drawing type is valid for the current
3357    phase. If not, use 'vdW balls'. This is currently used only for setting a
3358    default when atoms are added to the atoms draw list.
3359    '''
3360    if typ in ('lines','vdW balls','sticks','balls & sticks','ellipsoids'):
3361        return typ
3362    # elif generalData.get('Type','') == 'macromolecular':
3363    #     if typ in ('backbone',):
3364    #         return typ
3365    return 'vdW balls'
3366
3367if __name__ == "__main__":
3368    # test variable descriptions
3369    for var in '0::Afrac:*',':1:Scale','1::dAx:0','::undefined':
3370        v = var.split(':')[2]
3371        print(var+':\t', getDescr(v),getVarStep(v))
3372    import sys; sys.exit()
3373    # test equation evaluation
3374    def showEQ(calcobj):
3375        print (50*'=')
3376        print (calcobj.eObj.expression+'='+calcobj.EvalExpression())
3377        for v in sorted(calcobj.varLookup):
3378            print ("  "+v+'='+calcobj.exprDict[v]+'='+calcobj.varLookup[v])
3379        # print '  Derivatives'
3380        # for v in calcobj.derivStep.keys():
3381        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
3382
3383    obj = ExpressionObj()
3384
3385    obj.expression = "A*np.exp(B)"
3386    obj.assgnVars =  {'B': '0::Afrac:1'}
3387    obj.freeVars =  {'A': [u'A', 0.5, True]}
3388    #obj.CheckVars()
3389    calcobj = ExpressionCalcObj(obj)
3390
3391    obj1 = ExpressionObj()
3392    obj1.expression = "A*np.exp(B)"
3393    obj1.assgnVars =  {'B': '0::Afrac:*'}
3394    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
3395    #obj.CheckVars()
3396    calcobj1 = ExpressionCalcObj(obj1)
3397
3398    obj2 = ExpressionObj()
3399    obj2.distance_stuff = np.array([[0,1],[1,-1]])
3400    obj2.expression = "Dist(1,2)"
3401    GSASIIpath.InvokeDebugOpts()
3402    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3403    calcobj2 = ExpressionCalcObj(obj2)
3404    calcobj2.SetupCalc(parmDict2)
3405    showEQ(calcobj2)
3406
3407    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
3408    print ('\nDict = '+parmDict1)
3409    calcobj.SetupCalc(parmDict1)
3410    showEQ(calcobj)
3411    calcobj1.SetupCalc(parmDict1)
3412    showEQ(calcobj1)
3413
3414    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
3415    print ('Dict = '+parmDict2)
3416    calcobj.SetupCalc(parmDict2)
3417    showEQ(calcobj)
3418    calcobj1.SetupCalc(parmDict2)
3419    showEQ(calcobj1)
3420    calcobj2.SetupCalc(parmDict2)
3421    showEQ(calcobj2)
Note: See TracBrowser for help on using the repository browser.