source: trunk/GSASIIobj.py @ 3095

Last change on this file since 3095 was 3095, checked in by vondreele, 4 years ago

add new confit parm: Show_timing
enable editing of the Use column in seq results table; doesn't seem to affect plot tho.
always print Found SVD zeros in seq refinement as well
add local directory to path for finding fit equation functions
add a pretranslate vector to atom transformations - still needs work tho.
couple of TODOs in G2strMain for fix parameters in seq refinements
change 'debug' to 'Show_timing' in G2strMath

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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2017-09-21 19:42:50 +0000 (Thu, 21 Sep 2017) $
5# $Author: vondreele $
6# $Revision: 3095 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 3095 2017-09-21 19:42:50Z vondreele $
9########### SVN repository information ###################
10
11'''
12*GSASIIobj: Data objects*
13=========================
14
15This module defines and/or documents the data structures used in GSAS-II, as well
16as provides misc. support routines.
17
18Constraints Tree Item
19----------------------
20
21.. _Constraints_table:
22
23.. index::
24   single: Constraints object description
25   single: Data object descriptions; Constraints
26
27Constraints are stored in a dict, separated into groups.
28Note that parameter are named in the following pattern,
29p:h:<var>:n, where p is the phase number, h is the histogram number
30<var> is a variable name and n is the parameter number.
31If a parameter does not depend on a histogram or phase or is unnumbered, that
32number is omitted.
33Note that the contents of each dict item is a List where each element in the
34list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
35The constraints in this form are converted in
36:func:`GSASIIstrIO.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
37
38The keys in the Constraints dict are:
39
40.. tabularcolumns:: |l|p{4.5in}|
41
42==========  ====================================================
43  key         explanation
44==========  ====================================================
45Hist        This specifies a list of constraints on
46            histogram-related parameters,
47            which will be of form :h:<var>:n.
48HAP         This specifies a list of constraints on parameters
49            that are defined for every histogram in each phase
50            and are of form p:h:<var>:n.
51Phase       This specifies a list of constraints on phase
52            parameters,
53            which will be of form p::<var>:n.
54Global      This specifies a list of constraints on parameters
55            that are not tied to a histogram or phase and
56            are of form ::<var>:n
57==========  ====================================================
58
59.. _Constraint_definitions_table:
60
61.. index::
62   single: Constraint definition object description
63   single: Data object descriptions; Constraint Definition
64
65Each constraint is defined as an item in a list. Each constraint is of form::
66
67[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
68
69Where the variable pair list item containing two values [<mult>, <var>], where:
70
71  * <mult> is a multiplier for the constraint (float)
72  * <var> a :class:`G2VarObj` object (previously a str variable name of form
73      'p:h:name[:at]')
74
75Note that the last three items in the list play a special role:
76
77 * <fixedval> is the fixed value for a `constant equation` (``constype=c``)
78   constraint or is None. For a `New variable` (``constype=f``) constraint,
79   a variable name can be specified as a str (used for externally
80   generated constraints)
81 * <varyflag> is True or False for `New variable` (``constype=f``) constraints
82   or is None. This will be implemented in the future to indicate if these variables
83   should be refined.
84 * <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
85
86    * 'e' defines a set of equivalent variables. Only the first variable is refined (if the
87      appropriate refine flag is set) and and all other equivalent variables in the list
88      are generated from that variable, using the appropriate multipliers.
89    * 'c' defines a constraint equation of form,
90      :math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
91    * 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
92      even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
93      constraint and the mult value is ignored.
94      This is of particular value when needing to hold one or more variables where a
95      single flag controls a set of variables such as, coordinates,
96      the reciprocal metric tensor or anisotropic displacement parameter.
97    * 'f' defines a new variable (function) according to relationship
98      :math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
99
100Covariance Tree Item
101--------------------
102
103.. _Covariance_table:
104
105.. index::
106   single: Covariance description
107   single: Data object descriptions; Covariance
108
109The Covariance tree item has results from the last least-squares run. They
110are stored in a dict with these keys:
111
112.. tabularcolumns:: |l|l|p{4in}|
113
114=============  ===============  ====================================================
115  key            sub-key        explanation
116=============  ===============  ====================================================
117newCellDict    \                dict with lattice parameters computed by
118                                :func:`GSASIIstrMath.GetNewCellParms` (dict)
119title          \                Name of gpx file(?) (str)
120variables      \                Values for all N refined variables
121                                (list of float values, length N,
122                                ordered to match varyList)
123sig            \                Uncertainty values for all N refined variables
124                                (list of float values, length N,
125                                ordered to match varyList)
126varyList       \                List of directly refined variables
127                                (list of str values, length N)
128newAtomDict    \                dict with atom position values computed in
129                                :func:`GSASIIstrMath.ApplyXYZshifts` (dict)
130Rvals          \                R-factors, GOF, Marquardt value for last
131                                refinement cycle (dict)
132\              Nobs             Number of observed data points (int)
133\              Rwp              overall weighted profile R-factor (%, float)
134\              chisq            sum[w*(Iobs-Icalc)**2] for all data
135                                note this is not the reduced chi squared (float)
136\              lamMax           Marquardt value applied to Hessian diagonal
137                                (float)
138\              GOF              The goodness-of-fit, aka square root of
139                                the reduced chi squared. (float)
140covMatrix      \                The (NxN) covVariance matrix (np.array)
141=============  ===============  ====================================================
142
143Phase Tree Items
144----------------
145
146.. _Phase_table:
147
148.. index::
149   single: Phase object description
150   single: Data object descriptions; Phase
151
152Phase information is stored in the GSAS-II data tree as children of the
153Phases item in a dict with keys:
154
155.. tabularcolumns:: |l|l|p{4in}|
156
157==========  ===============  ====================================================
158  key         sub-key        explanation
159==========  ===============  ====================================================
160General         \            Overall information for the phase (dict)
161  \         AtomPtrs         list of four locations to use to pull info
162                             from the atom records (list)
163  \         F000X            x-ray F(000) intensity (float)
164  \         F000N            neutron F(000) intensity (float)
165  \         Mydir            directory of current .gpx file (str)
166  \         MCSA controls    Monte Carlo-Simulated Annealing controls (dict)
167  \         Cell             List with 8 items: cell refinement flag (bool)
168                             a, b, c, (Angstrom, float)
169                             alpha, beta & gamma (degrees, float)
170                             volume (A^3, float)
171  \         Type             'nuclear' or 'macromolecular' for now (str)
172  \         Map              dict of map parameters
173  \         SH Texture       dict of spherical harmonic preferred orientation
174                             parameters
175  \         Isotope          dict of isotopes for each atom type
176  \         Isotopes         dict of scattering lengths for each isotope
177                             combination for each element in phase
178  \         Name             phase name (str)
179  \         SGData           Space group details as a :ref:`space group (SGData) object <SGData_table>`
180                             as defined in :func:`GSASIIspc.SpcGroup`.
181  \         Pawley neg wt    Restraint value for negative Pawley intensities
182                             (float)
183  \         Flip             dict of Charge flip controls
184  \         Data plot type   data plot type ('Mustrain', 'Size' or
185                             'Preferred orientation') for powder data (str)
186  \         Mass             Mass of unit cell contents in g/mol
187  \         POhkl            March-Dollase preferred orientation direction
188  \         Z                dict of atomic numbers for each atom type
189  \         vdWRadii         dict of van der Waals radii for each atom type
190  \         Color            Colors for atoms (list of (r,b,g) triplets)
191  \         AtomTypes        List of atom types
192  \         AtomMass         List of masses for atoms
193  \         doPawley         Flag for Pawley intensity extraction (bool)
194  \         NoAtoms          Number of atoms per unit cell of each type (dict)
195  \         Pawley dmin      maximum Q (as d-space) to use for Pawley
196                             extraction (float)
197  \         BondRadii        Default radius for each atom used to compute
198                             interatomic distances (list of floats)
199  \         AngleRadii       Default radius for each atom used to compute
200                             interatomic angles (list of floats)
201  \         DisAglCtls       Dict with distance/angle search controls,
202                             which has keys 'Name', 'AtomTypes',
203                             'BondRadii', 'AngleRadii' which are as above
204                             except are possibly edited. Also contains
205                             'Factors', which is a 2 element list with
206                             a multiplier for bond and angle search range
207                             [typically (0.85,0.85)].
208ranId           \            unique random number Id for phase (int)
209pId             \            Phase Id number for current project (int).
210Atoms           \            Atoms in phase as a list of lists. The outer list
211                             is for each atom, the inner list contains varying
212                             items depending on the type of phase, see
213                             the :ref:`Atom Records <Atoms_table>` description.
214                             (list of lists)
215Drawing         \            Display parameters (dict)
216\           ballScale        Size of spheres in ball-and-stick display (float)
217\           bondList         dict with bonds
218\           contourLevel     map contour level in e/A^3 (float)
219\           showABC          Flag to show view point triplet (bool). True=show.
220\           viewDir          cartesian viewing direction (np.array with three
221                             elements)
222\           Zclip            clipping distance in A (float)
223\           backColor        background for plot as and R,G,B triplet
224                             (default = [0, 0, 0], black).
225                             (list with three atoms)
226\           selectedAtoms    List of selected atoms (list of int values)
227\           showRigidBodies  Flag to highlight rigid body placement
228\           sizeH            Size ratio for H atoms (float)
229\           bondRadius       Size of binds in A (float)
230\           atomPtrs         positions of x, type, site sym, ADP flag in Draw Atoms (list)
231\           viewPoint        list of lists. First item in list is [x,y,z]
232                             in fractional coordinates for the center of
233                             the plot. Second item list of previous & current
234                             atom number viewed (may be [0,0])
235\           showHydrogen     Flag to control plotting of H atoms.
236\           unitCellBox      Flag to control display of the unit cell.
237\           ellipseProb      Probability limit for display of thermal
238                             ellipsoids in % (float).
239\           vdwScale         Multiplier of van der Waals radius for
240                             display of vdW spheres.
241\           Atoms            A list of lists with an entry for each atom
242                             that is plotted.
243\           Zstep            Step to de/increase Z-clip (float)
244\           Quaternion       Viewing quaternion (4 element np.array)
245\           radiusFactor     Distance ratio for searching for bonds. ? Bonds
246                             are located that are within r(Ra+Rb) and (Ra+Rb)/r
247                             where Ra and Rb are the atomic radii.
248\           oldxy            previous view point (list with two floats)
249\           cameraPos        Viewing position in A for plot (float)
250\           depthFog         True if use depthFog on plot - set currently as False (bool)
251RBModels        \            Rigid body assignments (note Rigid body definitions
252                             are stored in their own main top-level tree entry.)
253Pawley ref      \            Pawley reflections
254Histograms      \            A dict of dicts. The key for the outer dict is
255                             the histograms tied to this phase. The inner
256                             dict contains the combined phase/histogram
257                             parameters for items such as scale factors,
258                             size and strain parameters. The following are the
259                             keys to the inner dict. (dict)
260\           Babinet          For protein crystallography. Dictionary with two
261                             entries, 'BabA', 'BabU'
262\           Extinction       Extinction parameter (list of float, bool)
263\           HStrain          Hydrostatic strain. List of two lists. The first is
264                             a list of the HStrain parameters (1, 2, 3, 4, or 6
265                             depending on unit cell), the second is a list of boolean
266                             refinement parameters (same length)
267\           Histogram        The name of the associated histogram (str)
268\           LeBail           Flag for LeBail extraction (bool)
269\           Mustrain         List of microstrain parameters, in order:
270
271                               0. Type, one of u'generalized', u'isotropic',
272                                  u'uniaxial'
273                               1. Isotropic/uniaxial parameters - list of 3 floats
274                               2. Refinement flags - list of 3 bools
275                               3. Microstrain axis - list of 3 ints, [h, k, l]
276                               4. Generalized mustrain parameters - list of 2-6
277                                  floats, depending on space group
278                               5. Generalized refinement flags - list of bools,
279                                  corresponding to the parameters of (4)
280\           Pref.Ori.        Preferred Orientation. List of eight parameters.
281                             Items marked SH are only used for Spherical Harmonics.
282
283                               0. Type, 'MD' for March-Dollase or 'SH' for
284                                  Spherical Harmonics
285                               1. Value, float
286                               2. Refinement flag, bool
287                               3. Preferred direction, list of ints, [h, k, l]
288                               4. SH - number of terms, int
289                               5. SH - dict
290                               6. SH - list
291                               7. SH - float
292\           Scale            Phase fraction, list of [float, bool].
293\           Show             bool
294\           Use              bool
295\           newLeBail        Whether to perform a new LeBail extraction
296MCSA            \            Monte-Carlo simulated annealing parameters (dict)
297\
298==========  ===============  ====================================================
299
300Rigid Body Objects
301------------------
302
303.. _RBData_table:
304
305.. index::
306   single: Rigid Body Data description
307   single: Data object descriptions; Rigid Body Data
308
309Rigid body descriptions are available for two types of rigid bodies: 'Vector'
310and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
311with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
312with defined refinable torsion angles.
313
314.. tabularcolumns:: |l|l|p{4in}|
315
316==========  ===============  ====================================================
317  key         sub-key        explanation
318==========  ===============  ====================================================
319Vector      RBId             vector rigid bodies (dict of dict)
320\           AtInfo           Drad, Color: atom drawing radius & color for each atom type (dict)
321\           RBname           Name assigned by user to rigid body (str)
322\           VectMag          vector magnitudes in A (list)
323\           rbXYZ            Cartesian coordinates for Vector rigid body (list of 3 float)
324\           rbRef            3 assigned reference atom nos. in rigid body for origin
325                             definition, use center of atoms flag (list of 3 int & 1 bool)
326\           VectRef          refinement flags for VectMag values (list of bool)
327\           rbTypes          Atom types for each atom in rigid body (list of str)
328\           rbVect           Cartesian vectors for each translation used to build rigid body (list of lists)
329\           useCount         Number of times rigid body is used in any structure (int)
330Residue     RBId             residue rigid bodies (dict of dict)
331\           AtInfo           Drad, Color: atom drawing radius & color for each atom type(dict)
332\           RBname           Name assigned by user to rigid body (str)
333\           rbXYZ            Cartesian coordinates for Residue rigid body (list of 3 float)
334\           rbTypes          Atom types for each atom in rigid body (list of str)
335\           atNames          Names of each atom in rigid body (e.g. C1,N2...) (list of str)
336\           rbRef            3 assigned reference atom nos. in rigid body for origin
337                             definition, use center of atoms flag (list of 3 int & 1 bool)
338\           rbSeq            Orig,Piv,angle,Riding (list): definition of internal rigid body
339                             torsion; origin atom (int), pivot atom (int), torsion angle (float),
340                             riding atoms (list of int)
341\           SelSeq           [int,int] used by SeqSizer to identify objects
342\           useCount         Number of times rigid body is used in any structure (int)
343RBIds           \            unique Ids generated upon creation of each rigid body (dict)
344\           Vector           Ids for each Vector rigid body (list)
345\           Residue          Ids for each Residue rigid body (list)
346==========  ===============  ====================================================
347
348Space Group Objects
349-------------------
350
351.. _SGData_table:
352
353.. index::
354   single: Space Group Data description
355   single: Data object descriptions; Space Group Data
356
357Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
358and the information is placed in a SGdata object
359which is a dict with these keys:
360
361.. tabularcolumns:: |l|p{4.5in}|
362
363==========  ====================================================
364  key         explanation
365==========  ====================================================
366SpGrp       space group symbol (str)
367Laue        one of the following 14 Laue classes:
368            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
369            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
370SGInv       True if centrosymmetric, False if not (bool)
371SGLatt      Lattice centering type. Will be one of
372            P, A, B, C, I, F, R (str)
373SGUniq      unique axis if monoclinic. Will be
374            a, b, or c for monoclinic space groups.
375            Will be blank for non-monoclinic. (str)
376SGCen       Symmetry cell centering vectors. A (n,3) np.array
377            of centers. Will always have at least one row:
378            ``np.array([[0, 0, 0]])``
379SGOps       symmetry operations as a list of form
380            ``[[M1,T1], [M2,T2],...]``
381            where :math:`M_n` is a 3x3 np.array
382            and :math:`T_n` is a length 3 np.array.
383            Atom coordinates are transformed where the
384            Asymmetric unit coordinates [X is (x,y,z)]
385            are transformed using
386            :math:`X^\prime = M_n*X+T_n`
387SGSys       symmetry unit cell: type one of
388            'triclinic', 'monoclinic', 'orthorhombic',
389            'tetragonal', 'rhombohedral', 'trigonal',
390            'hexagonal', 'cubic' (str)
391SGPolax     Axes for space group polarity. Will be one of
392            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
393            'xyz'. In the case where axes are arbitrary
394            '111' is used (P 1, and ?).
395==========  ====================================================
396
397.. _SSGData_table:
398
399.. index::
400   single: Superspace Group Data description
401   single: Data object descriptions; Superspace Group Data
402
403Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
404and the information is placed in a SSGdata object
405which is a dict with these keys:
406
407.. tabularcolumns:: |l|p{4.5in}|
408
409==========  ====================================================
410  key         explanation
411==========  ====================================================
412SSpGrp      superspace group symbol extension to space group
413            symbol, accidental spaces removed
414SSGCen      4D cell centering vectors [0,0,0,0] at least
415SSGOps      4D symmetry operations as [M,T] so that M*x+T = x'
416==========  ====================================================
417
418
419Atom Records
420------------
421
422.. _Atoms_table:
423
424.. index::
425   single: Atoms record description
426   single: Data object descriptions; Atoms record
427
428
429If ``phasedict`` points to the phase information in the data tree, then
430atoms are contained in a list of atom records (list) in
431``phasedict['Atoms']``. Also needed to read atom information
432are four pointers, ``cx,ct,cs,cia = phasedict['General']['AtomPtrs']``,
433which define locations in the atom record, as shown below. Items shown are
434always present; additional ones for macromolecular phases are marked 'mm'
435
436.. tabularcolumns:: |l|p{4.5in}|
437
438==============   ====================================================
439location         explanation
440==============   ====================================================
441ct-4              mm - residue number (str)
442ct-3              mm - residue name (e.g. ALA) (str)
443ct-2              mm - chain label (str)
444ct-1              atom label (str)
445ct                atom type (str)
446ct+1              refinement flags; combination of 'F', 'X', 'U' (str)
447cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
448cx+3              site occupancy (float)
449cs                site symmetry (str)
450cs+1              site multiplicity (int)
451cia               ADP flag: Isotropic ('I') or Anisotropic ('A')
452cia+1             Uiso (float)
453cia+2...cia+7     U11, U22, U33, U12, U13, U23 (6 floats)
454atom[cia+8]       unique atom identifier (int)
455
456==============   ====================================================
457
458Drawing Atom Records
459--------------------
460
461.. _Drawing_atoms_table:
462
463.. index::
464   single: Drawing atoms record description
465   single: Data object descriptions; Drawing atoms record
466
467
468If ``phasedict`` points to the phase information in the data tree, then
469drawing atoms are contained in a list of drawing atom records (list) in
470``phasedict['Drawing']['Atoms']``. Also needed to read atom information
471are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
472which define locations in the atom record, as shown below. Items shown are
473always present; additional ones for macromolecular phases are marked 'mm'
474
475.. tabularcolumns:: |l|p{4.5in}|
476
477==============   ====================================================
478location         explanation
479==============   ====================================================
480ct-4              mm - residue number (str)
481ct-3              mm - residue name (e.g. ALA) (str)
482ct-2              mm - chain label (str)
483ct-1              atom label (str)
484ct                atom type (str)
485cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
486cs-1              Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str)
487cs                atom drawing style; e.g. 'balls & sticks' (str)
488cs+1              atom label style (e.g. 'name') (str)
489cs+2              atom color (RBG triplet) (int)
490cs+3              ADP flag: Isotropic ('I') or Anisotropic ('A')
491cs+4              Uiso (float)
492cs+5...cs+11      U11, U22, U33, U12, U13, U23 (6 floats)
493ci                unique atom identifier; matches source atom Id in Atom Records (int)
494==============   ====================================================
495
496Powder Diffraction Tree Items
497-----------------------------
498
499.. _Powder_table:
500
501.. index::
502   single: Powder data object description
503   single: Data object descriptions; Powder Data
504
505Every powder diffraction histogram is stored in the GSAS-II data tree
506with a top-level entry named beginning with the string "PWDR ". The
507diffraction data for that information are directly associated with
508that tree item and there are a series of children to that item. The
509routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
510and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
511load this information into a dictionary where the child tree name is
512used as a key, and the information in the main entry is assigned
513a key of ``Data``, as outlined below.
514
515.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
516
517======================  ===============  ====================================================
518  key                      sub-key        explanation
519======================  ===============  ====================================================
520Comments                      \           Text strings extracted from the original powder
521                                          data header. These cannot be changed by the user;
522                                          it may be empty.
523Limits                       \            A list of two two element lists, as [[Ld,Hd],[L,H]]
524                                          where L and Ld are the current and default lowest
525                                          two-theta value to be used and
526                                          where H and Hd are the current and default highest
527                                          two-theta value to be used.
528Reflection Lists              \           A dict with an entry for each phase in the
529                                          histogram. The contents of each dict item
530                                          is a dict containing reflections, as described in
531                                          the :ref:`Powder Reflections <PowderRefl_table>`
532                                          description.
533Instrument Parameters         \           A list containing two dicts where the possible
534                                          keys in each dict are listed below. The value
535                                          for each item is a list containing three values:
536                                          the initial value, the current value and a
537                                          refinement flag which can have a value of
538                                          True, False or 0 where 0 indicates a value that
539                                          cannot be refined. The first and second
540                                          values are floats unless otherwise noted.
541                                          Items in the first dict are noted as [1]
542\                         Lam             Specifies a wavelength in Angstroms [1]
543\                         Lam1            Specifies the primary wavelength in
544                                          Angstrom, when an alpha1, alpha2
545                                          source is used [1]
546\                         Lam2            Specifies the secondary wavelength in
547                                          Angstrom, when an alpha1, alpha2
548                                          source is used [1]
549                          I(L2)/I(L1)     Ratio of Lam2 to Lam1 [1]
550\                         Type            Histogram type (str) [1]:
551                                           * 'PXC' for constant wavelength x-ray
552                                           * 'PNC' for constant wavelength neutron
553                                           * 'PNT' for time of flight neutron
554\                         Zero            Two-theta zero correction in *degrees* [1]
555\                         Azimuth         Azimuthal setting angle for data recorded
556                                          with differing setting angles [1]
557\                         U, V, W         Cagliotti profile coefficients
558                                          for Gaussian instrumental broadening, where the
559                                          FWHM goes as
560                                          :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
561\                         X, Y            Cauchy (Lorentzian) instrumental broadening
562                                          coefficients [1]
563\                         SH/L            Variant of the Finger-Cox-Jephcoat asymmetric
564                                          peak broadening ratio. Note that this is the
565                                          average between S/L and H/L where S is
566                                          sample height, H is the slit height and
567                                          L is the goniometer diameter. [1]
568\                         Polariz.        Polarization coefficient. [1]
569wtFactor                      \           A weighting factor to increase or decrease
570                                          the leverage of data in the histogram (float).
571                                          A value of 1.0 weights the data with their
572                                          standard uncertainties and a larger value
573                                          increases the weighting of the data (equivalent
574                                          to decreasing the uncertainties).
575Sample Parameters             \           Specifies a dict with parameters that describe how
576                                          the data were collected, as listed
577                                          below. Refinable parameters are a list containing
578                                          a float and a bool, where the second value
579                                          specifies if the value is refined, otherwise
580                                          the value is a float unless otherwise noted.
581\                         Scale           The histogram scale factor (refinable)
582\                         Absorption      The sample absorption coefficient as
583                                          :math:`\\mu r` where r is the radius
584                                          (refinable). Only valid for Debye-Scherrer geometry.
585\                         SurfaceRoughA   Surface roughness parameter A as defined by
586                                          Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable -
587                                          only valid for Bragg-Brentano geometry)
588\                         SurfaceRoughB   Surface roughness parameter B (refinable -
589                                          only valid for Bragg-Brentano geometry)
590\                         DisplaceX,      Sample displacement from goniometer center
591                          DisplaceY       where Y is along the beam direction and
592                                          X is perpendicular. Units are :math:`\\mu m`
593                                          (refinable).
594\                         Phi, Chi,       Goniometer sample setting angles, in degrees.
595                          Omega
596\                         Gonio. radius   Radius of the diffractometer in mm
597\                         InstrName       A name for the instrument, used in preparing
598                                          a CIF (str).
599\                         Force,          Variables that describe how the measurement
600                          Temperature,    was performed. Not used directly in
601                          Humidity,       any computations.
602                          Pressure,
603                          Voltage
604\                         ranId           The random-number Id for the histogram
605                                          (same value as where top-level key is ranId)
606\                         Type            Type of diffraction data, may be 'Debye-Scherrer'
607                                          or 'Bragg-Brentano' (str).
608\                         Diffuse         not in use?
609hId                           \           The number assigned to the histogram when
610                                          the project is loaded or edited (can change)
611ranId                         \           A random number id for the histogram
612                                          that does not change
613Background                    \           The background is stored as a list with where
614                                          the first item in the list is list and the second
615                                          item is a dict. The list contains the background
616                                          function and its coefficients; the dict contains
617                                          Debye diffuse terms and background peaks.
618                                          (TODO: this needs to be expanded.)
619Data                          \           The data consist of a list of 6 np.arrays
620                                          containing in order:
621
622                                           0. the x-postions (two-theta in degrees),
623                                           1. the intensity values (Yobs),
624                                           2. the weights for each Yobs value
625                                           3. the computed intensity values (Ycalc)
626                                           4. the background values
627                                           5. Yobs-Ycalc
628======================  ===============  ====================================================
629
630Powder Reflection Data Structure
631--------------------------------
632
633.. _PowderRefl_table:
634
635.. index::
636   single: Powder reflection object description
637   single: Data object descriptions; Powder Reflections
638
639For every phase in a histogram, the ``Reflection Lists`` value is a dict
640one element of which is `'RefList'`, which is a np.array containing
641reflections. The columns in that array are documented below.
642
643==========  ====================================================
644  index         explanation
645==========  ====================================================
646 0,1,2       h,k,l (float)
647 3           multiplicity
648 4           d-space, Angstrom
649 5           pos, two-theta
650 6           sig, Gaussian width
651 7           gam, Lorenzian width
652 8           :math:`F_{obs}^2`
653 9           :math:`F_{calc}^2`
654 10          reflection phase, in degrees
655 11          intensity correction for reflection, this times
656             :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
657==========  ====================================================
658
659Single Crystal Tree Items
660-------------------------
661
662.. _Xtal_table:
663
664.. index::
665   single: Single Crystal data object description
666   single: Data object descriptions; Single crystal data
667
668Every single crystal diffraction histogram is stored in the GSAS-II data tree
669with a top-level entry named beginning with the string "HKLF ". The
670diffraction data for that information are directly associated with
671that tree item and there are a series of children to that item. The
672routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
673and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
674load this information into a dictionary where the child tree name is
675used as a key, and the information in the main entry is assigned
676a key of ``Data``, as outlined below.
677
678.. tabularcolumns:: |l|l|p{4in}|
679
680======================  ===============  ====================================================
681  key                      sub-key        explanation
682======================  ===============  ====================================================
683Data                          \           A dict that contains the
684                                          reflection table,
685                                          as described in the
686                                          :ref:`Single Crystal Reflections
687                                          <XtalRefl_table>`
688                                          description.
689
690Instrument Parameters         \           A list containing two dicts where the possible
691                                          keys in each dict are listed below. The value
692                                          for most items is a list containing two values:
693                                          the initial value, the current value.
694                                          The first and second
695                                          values are floats unless otherwise noted.
696\                         Lam             Specifies a wavelength in Angstroms (two floats)
697\                         Type            Histogram type (two str values):
698                                           * 'SXC' for constant wavelength x-ray
699                                           * 'SNC' for constant wavelength neutron
700                                           * 'SNT' for time of flight neutron
701\                         InstrName       A name for the instrument, used in preparing
702                                          a CIF (str).
703
704wtFactor                      \           A weighting factor to increase or decrease
705                                          the leverage of data in the histogram (float).
706                                          A value of 1.0 weights the data with their
707                                          standard uncertainties and a larger value
708                                          increases the weighting of the data (equivalent
709                                          to decreasing the uncertainties).
710
711hId                           \           The number assigned to the histogram when
712                                          the project is loaded or edited (can change)
713ranId                         \           A random number id for the histogram
714                                          that does not change
715======================  ===============  ====================================================
716
717Single Crystal Reflection Data Structure
718----------------------------------------
719
720.. _XtalRefl_table:
721
722.. index::
723   single: Single Crystal reflection object description
724   single: Data object descriptions; Single Crystal Reflections
725
726For every single crystal a histogram, the ``'Data'`` item contains
727the structure factors as an np.array in item `'RefList'`.
728The columns in that array are documented below.
729
730==========  ====================================================
731  index         explanation
732==========  ====================================================
733 0,1,2       h,k,l (float)
734 3           multiplicity
735 4           d-space, Angstrom
736 5           :math:`F_{obs}^2`
737 6           :math:`\sigma(F_{obs}^2)`
738 7           :math:`F_{calc}^2`
739 8           :math:`F_{obs}^2T`
740 9           :math:`F_{calc}^2T`
741 10          reflection phase, in degrees
742 11          intensity correction for reflection, this times
743             :math:`F_{obs}^2` or :math:`F_{calc}^2`
744             gives Iobs or Icalc
745==========  ====================================================
746
747Image Data Structure
748--------------------
749
750.. _Image_table:
751
752.. index::
753   image: Image data object description
754   image: Image object descriptions
755
756Every 2-dimensional image is stored in the GSAS-II data tree
757with a top-level entry named beginning with the string "IMG ". The
758image data are directly associated with that tree item and there
759are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
760and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
761load this information into a dictionary where the child tree name is
762used as a key, and the information in the main entry is assigned
763a key of ``Data``, as outlined below.
764
765.. tabularcolumns:: |l|l|p{4in}|
766
767======================  ======================  ====================================================
768  key                      sub-key              explanation
769======================  ======================  ====================================================
770Comments                       \                Text strings extracted from the original image data
771                                                header or a metafile. These cannot be changed by
772                                                the user; it may be empty.
773Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
774                                                value. Accomodates
775                                                detector orientations other than with the detector
776                                                X-axis
777                                                horizontal.
778\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
779                                                during image integration multiplied by value. It must have the same size/shape as
780                                                the integrated image. NB: value < 0 for subtraction.
781\                           calibrant           (str) The material used for determining the position/orientation
782                                                of the image. The data is obtained from :func:`ImageCalibrants`
783                                                and UserCalibrants.py (supplied by user).
784\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
785\                           calibskip           (int) The number of expected diffraction lines skipped during the last
786                                                calibration run.
787\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
788                                                strikes the detector plane as determined by calibration. This point
789                                                does not have to be within the limits of the detector boundaries.
790\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
791                                                of the image is at the center line otherwise it is at the leading edge.
792\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
793\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
794                                                calibration calculations. See pixLimit for details as how point is found.
795\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
796                                                ring offset at higher angles. Optionally determined by calibration.
797\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
798\                           distance            (float) The distance (mm) from sample to detector plane.
799\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
800                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
801                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
802                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
803                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
804\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
805\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
806\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
807                                                Required for texture calculations.
808\                           invert_x            (bool) If True display the image with the x-axis inverted.
809\                           invert_y            (bool) If True display the image with the y-axis inverted.
810\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
811\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
812\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
813                                                intensities obtained during integration.
814\                           outAzimuths         (int) The number of azimuth pie slices.
815\                           outChannels         (int) The number of 2-theta steps.
816\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
817\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
818                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
819                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
820                                                Locations are used to construct rings of points for calibration calcualtions.
821\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
822                                                integration using value.
823\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
824                                                diffraction ring with the same d-spacing (dsp)
825\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
826                                                selected by the user,
827\                           Range               (list) The minimum & maximum values of the image
828\                           rotation            (float) The angle between the x-axis and the vector about which the
829                                                detector is tilted. Constrained to -180 to 180 deg.
830\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
831                                                calculations.
832\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
833                                                to cause correction to be applied.
834\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
835\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
836\                           showLines           (bool) If True then isplay the integration limits to be used.
837\                           size                (list:int) The number of pixels on the image x & y axes
838\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
839\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
840\                           wavelength          (float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).
841
842Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
843                                                to be excluded from integration
844\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
845                                                of which is excluded from recalibration and integration. Only one frame is allowed.
846\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
847                                                from integration.
848\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
849                                                to be excluded from integration.
850\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
851                                                to be excluded from integration.
852\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
853                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.
854
855Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
856\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
857                                                These will be restricted by space group symmetry; result of strain fit refinement.
858\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
859\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
860                                                and are used to determine the strain tensor.
861                                                The dictionary items are:
862                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
863                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
864                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
865                                                'Esig': (list: float) Esds for Emat from fitting.
866                                                'pixLimit': (int) Search range to find highest point on ring for each data point
867                                                'cutoff': (float) I/Ib cutoff for searching.
868                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
869                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
870                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
871
872======================  ======================  ====================================================
873
874Parameter Dictionary
875-------------------------
876
877.. _parmDict_table:
878
879.. index::
880   single: Parameter dictionary
881
882The parameter dictionary contains all of the variable parameters for the refinement.
883The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
884It is prepared in two ways. When loaded from the tree
885(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
886:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
887the values are lists with two elements: ``[value, refine flag]``
888
889When loaded from the GPX file (in
890:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
891dict is the actual parameter value (usually a float, but sometimes a
892letter or string flag value (such as I or A for iso/anisotropic).
893
894
895*Classes and routines*
896----------------------
897
898'''
899import re
900import imp
901import random as ran
902import sys
903import os.path as ospath
904import cPickle
905import GSASIIpath
906import GSASIImath as G2mth
907import GSASIIspc as G2spc
908import numpy as np
909
910GSASIIpath.SetVersionNumber("$Revision: 3095 $")
911
912DefaultControls = {
913    'deriv type':'analytic Hessian',
914    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
915    'UsrReject':{'minF/sig':0.,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
916    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
917    'Author':'no name',
918    'FreePrm1':'Sample humidity (%)',
919    'FreePrm2':'Sample voltage (V)',
920    'FreePrm3':'Applied load (MN)',
921    'ShowCell':False,
922    }
923'''Values to be used as defaults for the initial contents of the ``Controls``
924data tree item.
925'''
926def StripUnicode(string,subs='.'):
927    '''Strip non-ASCII characters from strings
928
929    :param str string: string to strip Unicode characters from
930    :param str subs: character(s) to place into string in place of each
931      Unicode character. Defaults to '.'
932
933    :returns: a new string with only ASCII characters
934    '''
935    s = ''
936    for c in string:
937        if ord(c) < 128:
938            s += c
939        else:
940            s += subs
941    return s.encode('ascii','replace')
942
943def MakeUniqueLabel(lbl,labellist):
944    '''Make sure that every a label is unique against a list by adding
945    digits at the end until it is not found in list.
946
947    :param str lbl: the input label
948    :param list labellist: the labels that have already been encountered
949    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
950      ``_10-99``, etc.) appended at the end
951    '''
952    lbl = StripUnicode(lbl.strip(),'_')
953    if not lbl: # deal with a blank label
954        lbl = '_1'
955    if lbl not in labellist:
956        labellist.append(lbl)
957        return lbl
958    i = 1
959    prefix = lbl
960    if '_' in lbl:
961        prefix = lbl[:lbl.rfind('_')]
962        suffix = lbl[lbl.rfind('_')+1:]
963        try:
964            i = int(suffix)+1
965        except: # suffix could not be parsed
966            i = 1
967            prefix = lbl
968    while prefix+'_'+str(i) in labellist:
969        i += 1
970    else:
971        lbl = prefix+'_'+str(i)
972        labellist.append(lbl)
973    return lbl
974
975PhaseIdLookup = {}
976'''dict listing phase name and random Id keyed by sequential phase index as a str;
977best to access this using :func:`LookupPhaseName`
978'''
979PhaseRanIdLookup = {}
980'''dict listing phase sequential index keyed by phase random Id;
981best to access this using :func:`LookupPhaseId`
982'''
983HistIdLookup = {}
984'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
985best to access this using :func:`LookupHistName`
986'''
987HistRanIdLookup = {}
988'''dict listing histogram sequential index keyed by histogram random Id;
989best to access this using :func:`LookupHistId`
990'''
991AtomIdLookup = {}
992'''dict listing for each phase index as a str, the atom label and atom random Id,
993keyed by atom sequential index as a str;
994best to access this using :func:`LookupAtomLabel`
995'''
996AtomRanIdLookup = {}
997'''dict listing for each phase the atom sequential index keyed by atom random Id;
998best to access this using :func:`LookupAtomId`
999'''
1000ShortPhaseNames = {}
1001'''a dict containing a possibly shortened and when non-unique numbered
1002version of the phase name. Keyed by the phase sequential index.
1003'''
1004ShortHistNames = {}
1005'''a dict containing a possibly shortened and when non-unique numbered
1006version of the histogram name. Keyed by the histogram sequential index.
1007'''
1008
1009VarDesc = {}
1010''' This dictionary lists descriptions for GSAS-II variables,
1011as set in :func:`CompileVarDesc`. See that function for a description
1012for how keys and values are written.
1013'''
1014
1015reVarDesc = {}
1016''' This dictionary lists descriptions for GSAS-II variables with
1017the same values as :attr:`VarDesc` except that keys have been compiled as
1018regular expressions. Initialized in :func:`CompileVarDesc`.
1019'''
1020# create a default space group object for P1; N.B. fails when building documentation
1021try:
1022    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
1023except TypeError:
1024    pass
1025
1026def GetPhaseNames(fl):
1027    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
1028    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
1029
1030    :param file fl: opened .gpx file
1031    :return: list of phase names
1032    '''
1033    PhaseNames = []
1034    while True:
1035        try:
1036            data = cPickle.load(fl)
1037        except EOFError:
1038            break
1039        datum = data[0]
1040        if 'Phases' == datum[0]:
1041            for datus in data[1:]:
1042                PhaseNames.append(datus[0])
1043    fl.seek(0)          #reposition file
1044    return PhaseNames
1045
1046def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1047    '''Create a new phase dict with default values for various parameters
1048
1049    :param str Name: Name for new Phase
1050
1051    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1052      defaults to data for P 1
1053
1054    :param list cell: unit cell parameter list; defaults to
1055      [1.0,1.0,1.0,90.,90,90.,1.]
1056
1057    '''
1058    if SGData is None: SGData = P1SGData
1059    if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1060    phaseData = {
1061        'ranId':ran.randint(0,sys.maxint),
1062        'General':{
1063            'Name':Name,
1064            'Type':'nuclear',
1065            'Modulated':False,
1066            'AtomPtrs':[3,1,7,9],
1067            'SGData':SGData,
1068            'Cell':[False,]+cell,
1069            'Pawley dmin':1.0,
1070            'Data plot type':'None',
1071            'SH Texture':{
1072                'Order':0,
1073                'Model':'cylindrical',
1074                'Sample omega':[False,0.0],
1075                'Sample chi':[False,0.0],
1076                'Sample phi':[False,0.0],
1077                'SH Coeff':[False,{}],
1078                'SHShow':False,
1079                'PFhkl':[0,0,1],
1080                'PFxyz':[0,0,1],
1081                'PlotType':'Pole figure',
1082                'Penalty':[['',],0.1,False,1.0]}},
1083        'Atoms':[],
1084        'Drawing':{},
1085        'Histograms':{},
1086        'Pawley ref':[],
1087        'RBModels':{},
1088        }
1089    if Super and Super.get('Use',False):
1090        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1091        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1092        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1093
1094    return phaseData
1095
1096def ReadCIF(URLorFile):
1097    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1098    (from James Hester).
1099    The open routine gets confused with DOS names that begin with a letter and colon
1100    "C:\dir\" so this routine will try to open the passed name as a file and if that
1101    fails, try it as a URL
1102
1103    :param str URLorFile: string containing a URL or a file name. Code will try first
1104      to open it as a file and then as a URL.
1105
1106    :returns: a PyCifRW CIF object.
1107    '''
1108    import CifFile as cif # PyCifRW from James Hester
1109
1110    # alternate approach:
1111    #import urllib
1112    #ciffile = 'file:'+urllib.pathname2url(filename)
1113
1114    try:
1115        fp = open(URLorFile,'r')
1116        cf = cif.ReadCif(fp)
1117        fp.close()
1118        return cf
1119    except IOError:
1120        return cif.ReadCif(URLorFile)
1121
1122def IndexAllIds(Histograms,Phases):
1123    '''Scan through the used phases & histograms and create an index
1124    to the random numbers of phases, histograms and atoms. While doing this,
1125    confirm that assigned random numbers are unique -- just in case lightning
1126    strikes twice in the same place.
1127
1128    Note: this code assumes that the atom random Id (ranId) is the last
1129    element each atom record.
1130
1131    This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
1132    (which loads the histograms and phases from a GPX file),
1133    :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
1134    (which loads the histograms and phases from the data tree.) and
1135    :meth:`GSASIIconstrGUI.UpdateConstraints`
1136    (which displays & edits the constraints in a GUI)
1137
1138    TODO: do we need a lookup for rigid body variables?
1139    '''
1140    # process phases and atoms
1141    PhaseIdLookup.clear()
1142    PhaseRanIdLookup.clear()
1143    AtomIdLookup.clear()
1144    AtomRanIdLookup.clear()
1145    ShortPhaseNames.clear()
1146    for ph in Phases:
1147        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1148        ranId = Phases[ph]['ranId']
1149        while ranId in PhaseRanIdLookup:
1150            # Found duplicate random Id! note and reassign
1151            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1152            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxint)
1153        pId = str(Phases[ph]['pId'])
1154        PhaseIdLookup[pId] = (ph,ranId)
1155        PhaseRanIdLookup[ranId] = pId
1156        shortname = ph  #[:10]
1157        while shortname in ShortPhaseNames.values():
1158            shortname = ph[:8] + ' ('+ pId + ')'
1159        ShortPhaseNames[pId] = shortname
1160        AtomIdLookup[pId] = {}
1161        AtomRanIdLookup[pId] = {}
1162        for iatm,at in enumerate(Phases[ph]['Atoms']):
1163            ranId = at[cia+8]
1164            while ranId in AtomRanIdLookup[pId]: # check for dups
1165                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1166                at[cia+8] = ranId = ran.randint(0,sys.maxint)
1167            AtomRanIdLookup[pId][ranId] = str(iatm)
1168            if Phases[ph]['General']['Type'] == 'macromolecular':
1169                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1170            else:
1171                label = at[ct-1]
1172            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1173    # process histograms
1174    HistIdLookup.clear()
1175    HistRanIdLookup.clear()
1176    ShortHistNames.clear()
1177    for hist in Histograms:
1178        ranId = Histograms[hist]['ranId']
1179        while ranId in HistRanIdLookup:
1180            # Found duplicate random Id! note and reassign
1181            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1182            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxint)
1183        hId = str(Histograms[hist]['hId'])
1184        HistIdLookup[hId] = (hist,ranId)
1185        HistRanIdLookup[ranId] = hId
1186        shortname = hist[:15]
1187        while shortname in ShortHistNames.values():
1188            shortname = hist[:11] + ' ('+ hId + ')'
1189        ShortHistNames[hId] = shortname
1190
1191def LookupAtomId(pId,ranId):
1192    '''Get the atom number from a phase and atom random Id
1193
1194    :param int/str pId: the sequential number of the phase
1195    :param int ranId: the random Id assigned to an atom
1196
1197    :returns: the index number of the atom (str)
1198    '''
1199    if not AtomRanIdLookup:
1200        raise Exception,'Error: LookupAtomId called before IndexAllIds was run'
1201    if pId is None or pId == '':
1202        raise KeyError,'Error: phase is invalid (None or blank)'
1203    pId = str(pId)
1204    if pId not in AtomRanIdLookup:
1205        raise KeyError,'Error: LookupAtomId does not have phase '+pId
1206    if ranId not in AtomRanIdLookup[pId]:
1207        raise KeyError,'Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']'
1208    return AtomRanIdLookup[pId][ranId]
1209
1210def LookupAtomLabel(pId,index):
1211    '''Get the atom label from a phase and atom index number
1212
1213    :param int/str pId: the sequential number of the phase
1214    :param int index: the index of the atom in the list of atoms
1215
1216    :returns: the label for the atom (str) and the random Id of the atom (int)
1217    '''
1218    if not AtomIdLookup:
1219        raise Exception,'Error: LookupAtomLabel called before IndexAllIds was run'
1220    if pId is None or pId == '':
1221        raise KeyError,'Error: phase is invalid (None or blank)'
1222    pId = str(pId)
1223    if pId not in AtomIdLookup:
1224        raise KeyError,'Error: LookupAtomLabel does not have phase '+pId
1225    if index not in AtomIdLookup[pId]:
1226        raise KeyError,'Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']'
1227    return AtomIdLookup[pId][index]
1228
1229def LookupPhaseId(ranId):
1230    '''Get the phase number and name from a phase random Id
1231
1232    :param int ranId: the random Id assigned to a phase
1233    :returns: the sequential Id (pId) number for the phase (str)
1234    '''
1235    if not PhaseRanIdLookup:
1236        raise Exception,'Error: LookupPhaseId called before IndexAllIds was run'
1237    if ranId not in PhaseRanIdLookup:
1238        raise KeyError,'Error: LookupPhaseId does not have ranId '+str(ranId)
1239    return PhaseRanIdLookup[ranId]
1240
1241def LookupPhaseName(pId):
1242    '''Get the phase number and name from a phase Id
1243
1244    :param int/str pId: the sequential assigned to a phase
1245    :returns:  (phase,ranId) where phase is the name of the phase (str)
1246      and ranId is the random # id for the phase (int)
1247    '''
1248    if not PhaseIdLookup:
1249        raise Exception,'Error: LookupPhaseName called before IndexAllIds was run'
1250    if pId is None or pId == '':
1251        raise KeyError,'Error: phase is invalid (None or blank)'
1252    pId = str(pId)
1253    if pId not in PhaseIdLookup:
1254        raise KeyError,'Error: LookupPhaseName does not have index '+pId
1255    return PhaseIdLookup[pId]
1256
1257def LookupHistId(ranId):
1258    '''Get the histogram number and name from a histogram random Id
1259
1260    :param int ranId: the random Id assigned to a histogram
1261    :returns: the sequential Id (hId) number for the histogram (str)
1262    '''
1263    if not HistRanIdLookup:
1264        raise Exception,'Error: LookupHistId called before IndexAllIds was run'
1265    if ranId not in HistRanIdLookup:
1266        raise KeyError,'Error: LookupHistId does not have ranId '+str(ranId)
1267    return HistRanIdLookup[ranId]
1268
1269def LookupHistName(hId):
1270    '''Get the histogram number and name from a histogram Id
1271
1272    :param int/str hId: the sequential assigned to a histogram
1273    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1274      and ranId is the random # id for the histogram (int)
1275    '''
1276    if not HistIdLookup:
1277        raise Exception,'Error: LookupHistName called before IndexAllIds was run'
1278    if hId is None or hId == '':
1279        raise KeyError,'Error: histogram is invalid (None or blank)'
1280    hId = str(hId)
1281    if hId not in HistIdLookup:
1282        raise KeyError,'Error: LookupHistName does not have index '+hId
1283    return HistIdLookup[hId]
1284
1285def fmtVarDescr(varname):
1286    '''Return a string with a more complete description for a GSAS-II variable
1287
1288    :param str varname: A full G2 variable name with 2 or 3 or 4
1289       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1290
1291    :returns: a string with the description
1292    '''
1293    s,l = VarDescr(varname)
1294    return s+": "+l
1295
1296def VarDescr(varname):
1297    '''Return two strings with a more complete description for a GSAS-II variable
1298
1299    :param str name: A full G2 variable name with 2 or 3 or 4
1300       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1301
1302    :returns: (loc,meaning) where loc describes what item the variable is mapped
1303      (phase, histogram, etc.) and meaning describes what the variable does.
1304    '''
1305
1306    # special handling for parameter names without a colons
1307    # for now, assume self-defining
1308    if varname.find(':') == -1:
1309        return "Global",varname
1310
1311    l = getVarDescr(varname)
1312    if not l:
1313        return ("invalid variable name ("+str(varname)+")!"),""
1314#        return "invalid variable name!",""
1315
1316    if not l[-1]:
1317        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1318
1319    if len(l) == 3:         #SASD variable name!
1320        s = 'component:'+l[1]
1321        return s,l[-1]
1322    s = ""
1323    if l[0] is not None and l[1] is not None: # HAP: keep short
1324        if l[2] == "Scale": # fix up ambigous name
1325            l[5] = "Phase fraction"
1326        if l[0] == '*':
1327            lbl = 'Seq. ref.'
1328        else:
1329            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1330        if l[1] == '*':
1331            hlbl = 'Seq. ref.'
1332        else:
1333            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1334        if hlbl[:4] == 'HKLF':
1335            hlbl = 'Xtl='+hlbl[5:]
1336        elif hlbl[:4] == 'PWDR':
1337            hlbl = 'Pwd='+hlbl[5:]
1338        else:
1339            hlbl = 'Hist='+hlbl
1340        s = "Ph="+str(lbl)+" * "+str(hlbl)
1341    else:
1342        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1343            l[5] = "Scale factor"
1344        if l[2] == 'Back': # background parameters are "special", alas
1345            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1346            l[-1] += ' #'+str(l[3])
1347        elif l[4] is not None: # rigid body parameter or modulation parm
1348            lbl = ShortPhaseNames.get(l[0],'phase?')
1349            if 'RB' in l[2]:    #rigid body parm
1350                s = "Res #"+str(l[3])+" body #"+str(l[4])+" in "+str(lbl)
1351            else: #modulation parm
1352                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1353        elif l[3] is not None: # atom parameter,
1354            lbl = ShortPhaseNames.get(l[0],'phase?')
1355            try:
1356                albl = LookupAtomLabel(l[0],l[3])[0]
1357            except KeyError:
1358                albl = 'Atom?'
1359            s = "Atom "+str(albl)+" in "+str(lbl)
1360        elif l[0] == '*':
1361            s = "All phases "
1362        elif l[0] is not None:
1363            lbl = ShortPhaseNames.get(l[0],'phase?')
1364            s = "Phase "+str(lbl)
1365        elif l[1] == '*':
1366            s = 'All hists'
1367        elif l[1] is not None:
1368            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1369            if hlbl[:4] == 'HKLF':
1370                hlbl = 'Xtl='+hlbl[5:]
1371            elif hlbl[:4] == 'PWDR':
1372                hlbl = 'Pwd='+hlbl[5:]
1373            else:
1374                hlbl = 'Hist='+hlbl
1375            s = str(hlbl)
1376    if not s:
1377        s = 'Global'
1378    return s,l[-1]
1379
1380def getVarDescr(varname):
1381    '''Return a short description for a GSAS-II variable
1382
1383    :param str name: A full G2 variable name with 2 or 3 or 4
1384       colons (<p>:<h>:name[:<a1>][:<a2>])
1385
1386    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1387      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1388      the histogram number and the atom number; `name` will always be
1389      a str; and `description` is str or `None`.
1390      If the variable name is incorrectly formed (for example, wrong
1391      number of colons), `None` is returned instead of a list.
1392    '''
1393    l = varname.split(':')
1394    if len(l) == 2:     #SASD parameter name
1395        return varname,l[0],getDescr(l[1])
1396    if len(l) == 3:
1397        l += [None,None]
1398    elif len(l) == 4:
1399        l += [None]
1400    elif len(l) != 5:
1401        return None
1402    for i in (0,1,3,4):
1403        if l[i] == "":
1404            l[i] = None
1405    l += [getDescr(l[2])]
1406    return l
1407
1408def CompileVarDesc():
1409    '''Set the values in the variable description lookup table (:attr:`VarDesc`)
1410    into :attr:`reVarDesc`. This is called in :func:`getDescr` so the initialization
1411    is always done before use.
1412
1413    Note that keys may contain regular expressions, where '[xyz]'
1414    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range of values).
1415    '.*' matches any string. For example::
1416
1417    'AUiso':'Atomic isotropic displacement parameter',
1418
1419    will match variable ``'p::AUiso:a'``.
1420    If parentheses are used in the key, the contents of those parentheses can be
1421    used in the value, such as::
1422
1423    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1424
1425    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1426    in the value when used.
1427
1428    '''
1429    if reVarDesc: return # already done
1430    for key,value in {
1431        # derived or other sequential vars
1432        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1433        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1434        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1435        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1436        # ambiguous, alas:
1437        'Scale' : 'Phase or Histogram scale factor',
1438        # Phase vars (p::<var>)
1439        'A([0-5])' : 'Reciprocal metric tensor component \\1',
1440        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1441        # Atom vars (p::<var>:a)
1442        'dA([xyz])$' : 'change to atomic coordinate, \\1',
1443        'A([xyz])$' : '\\1 fractional atomic coordinate',
1444        'AUiso':'Atomic isotropic displacement parameter',
1445        'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1446        'Afrac': 'Atomic site fraction parameter',
1447        'Amul': 'Atomic site multiplicity value',
1448        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1449        # Hist & Phase (HAP) vars (p:h:<var>)
1450        'Back': 'Background term',
1451        'BkPkint;(.*)':'Background peak #\\1 intensity',
1452        'BkPkpos;(.*)':'Background peak #\\1 position',
1453        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1454        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1455        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1456        'D([123][123])' : 'Anisotropic strain coef. \\1',
1457        'Extinction' : 'Extinction coef.',
1458        'MD' : 'March-Dollase coef.',
1459        'Mustrain;.*' : 'Microstrain coef.',
1460        'Size;.*' : 'Crystallite size value',
1461        'eA$' : 'Cubic mustrain value',
1462        'Ep$' : 'Primary extinction',
1463        'Es$' : 'Secondary type II extinction',
1464        'Eg$' : 'Secondary type I extinction',
1465        'Flack' : 'Flack parameter',
1466        'TwinFr' : 'Twin fraction',
1467        #Histogram vars (:h:<var>)
1468        'Absorption' : 'Absorption coef.',
1469        'Displace([XY])' : 'Debye-Scherrer sample displacement \\1',
1470        'Lam' : 'Wavelength',
1471        'Polariz\.' : 'Polarization correction',
1472        'SH/L' : 'FCJ peak asymmetry correction',
1473        '([UVW])$' : 'Gaussian instrument broadening \\1',
1474        '([XY])$' : 'Cauchy instrument broadening \\1',
1475        'Zero' : 'Debye-Scherrer zero correction',
1476        'nDebye' : 'Debye model background corr. terms',
1477        'nPeaks' : 'Fixed peak background corr. terms',
1478        'RBV.*' : 'Vector rigid body parameter',
1479        'RBR.*' : 'Residue rigid body parameter',
1480        'RBRO([aijk])' : 'Residue rigid body orientation parameter',
1481        'RBRP([xyz])' : 'Residue rigid body position parameter',
1482        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1483        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1484        'constr([0-9]*)' : 'Parameter from constraint',
1485        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1486        'mV([0-2])$' : 'Modulation vector component \\1',
1487        'Fsin'  :   'Sin site fraction modulation',
1488        'Fcos'  :   'Cos site fraction modulation',
1489        'Fzero'  :   'Crenel function offset',      #may go away
1490        'Fwid'   :   'Crenel function width',
1491        'Tmin'   :   'ZigZag/Block min location',
1492        'Tmax'   :   'ZigZag/Block max location',
1493        '([XYZ])max': 'ZigZag/Block max value for \\1',
1494        '([XYZ])sin'  : 'Sin position wave for \\1',
1495        '([XYZ])cos'  : 'Cos position wave for \\1',
1496        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1497        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1498        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1499        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1500        # PDF peak parms (l:<var>;l = peak no.)
1501        'PDFpos'  : 'PDF peak position',
1502        'PDFmag'  : 'PDF peak magnitude',
1503        'PDFsig'  : 'PDF peak std. dev.',
1504        # SASD vars (l:<var>;l = component)
1505        'Aspect ratio' : 'Particle aspect ratio',
1506        'Length' : 'Cylinder length',
1507        'Diameter' : 'Cylinder/disk diameter',
1508        'Thickness' : 'Disk thickness',
1509        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1510        'Dist' : 'Interparticle distance',
1511        'VolFr' : 'Dense scatterer volume fraction',
1512        'epis' : 'Sticky sphere epsilon',
1513        'Sticky' : 'Stickyness',
1514        'Depth' : 'Well depth',
1515        'Width' : 'Well width',
1516        'Volume' : 'Particle volume',
1517        'Radius' : 'Sphere/cylinder/disk radius',
1518        'Mean' : 'Particle mean radius',
1519        'StdDev' : 'Standard deviation in Mean',
1520        'G$': 'Guinier prefactor',
1521        'Rg$': 'Guinier radius of gyration',
1522        'B$': 'Porod prefactor',
1523        'P$': 'Porod power',
1524        'Cutoff': 'Porod cutoff',
1525        'PkInt': 'Bragg peak intensity',
1526        'PkPos': 'Bragg peak position',
1527        'PkSig': 'Bragg peak sigma',
1528        'PkGam': 'Bragg peak gamma',
1529        'e([12][12])' : 'strain tensor e\1',   # strain vars e11, e22, e12
1530        'Dcalc': 'Calc. d-spacing',
1531        'Back$': 'background parameter',
1532        'pos$': 'peak position',
1533        'int$': 'peak intensity',
1534        'WgtFrac':'phase weight fraction',
1535        'C\([0-9]*,[0-9]*\)' : 'spherical harmonics preferred orientation coef.',
1536        }.items():
1537        VarDesc[key] = value
1538        reVarDesc[re.compile(key)] = value
1539
1540def getDescr(name):
1541    '''Return a short description for a GSAS-II variable
1542
1543    :param str name: The descriptive part of the variable name without colons (:)
1544
1545    :returns: a short description or None if not found
1546    '''
1547
1548    CompileVarDesc() # compile the regular expressions, if needed
1549    for key in reVarDesc:
1550        m = key.match(name)
1551        if m:
1552            reVarDesc[key]
1553            return m.expand(reVarDesc[key])
1554    return None
1555
1556def GenWildCard(varlist):
1557    '''Generate wildcard versions of G2 variables. These introduce '*'
1558    for a phase, histogram or atom number (but only for one of these
1559    fields) but only when there is more than one matching variable in the
1560    input variable list. So if the input is this::
1561
1562      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
1563
1564    then the output will be this::
1565
1566       wildList = ['*::AUiso:0', '0::AUiso:*']
1567
1568    :param list varlist: an input list of GSAS-II variable names
1569      (such as 0::AUiso:0)
1570
1571    :returns: wildList, the generated list of wild card variable names.
1572    '''
1573    wild = []
1574    for i in (0,1,3):
1575        currentL = varlist[:]
1576        while currentL:
1577            item1 = currentL.pop(0)
1578            i1splt = item1.split(':')
1579            if i >= len(i1splt): continue
1580            if i1splt[i]:
1581                nextL = []
1582                i1splt[i] = '[0-9]+'
1583                rexp = re.compile(':'.join(i1splt))
1584                matchlist = [item1]
1585                for nxtitem in currentL:
1586                    if rexp.match(nxtitem):
1587                        matchlist += [nxtitem]
1588                    else:
1589                        nextL.append(nxtitem)
1590                if len(matchlist) > 1:
1591                    i1splt[i] = '*'
1592                    wild.append(':'.join(i1splt))
1593                currentL = nextL
1594    return wild
1595
1596def LookupWildCard(varname,varlist):
1597    '''returns a list of variable names from list varname
1598    that match wildcard name in varname
1599
1600    :param str varname: a G2 variable name containing a wildcard
1601      (such as \*::var)
1602    :param list varlist: the list of all variable names used in
1603      the current project
1604    :returns: a list of matching GSAS-II variables (may be empty)
1605    '''
1606    rexp = re.compile(varname.replace('*','[0-9]+'))
1607    return sorted([var for var in varlist if rexp.match(var)])
1608
1609
1610def _lookup(dic,key):
1611    '''Lookup a key in a dictionary, where None returns an empty string
1612    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
1613    '''
1614    if key is None:
1615        return ""
1616    elif key == "*":
1617        return "*"
1618    else:
1619        return dic.get(key,'?')
1620
1621def SortVariables(varlist):
1622    '''Sorts variable names in a sensible manner
1623    '''
1624    def cvnnums(var):
1625        v = []
1626        for i in var.split(':'):
1627            try:
1628                v.append(int(i))
1629            except:
1630                v.append(i)
1631        return v
1632    return sorted(varlist,key=cvnnums)
1633
1634class G2VarObj(object):
1635    '''Defines a GSAS-II variable either using the phase/atom/histogram
1636    unique Id numbers or using a character string that specifies
1637    variables by phase/atom/histogram number (which can change).
1638    Note that :func:`LoadID` should be used to (re)load the current Ids
1639    before creating or later using the G2VarObj object.
1640
1641    This can store rigid body variables, but does not translate the residue # and
1642    body # to/from random Ids
1643
1644    A :class:`G2VarObj` object can be created with a single parameter:
1645
1646    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
1647      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
1648
1649     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
1650     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
1651     * a is the atom number (which may be left blank in which case the third colon is omitted).
1652       The atom number can be specified as '*' if a phase number is specified (not as '*').
1653       For rigid body variables, specify a will be a string of form "residue:body#"
1654
1655      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
1656      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
1657      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
1658      For a rigid body variables, AtomID is a string of form "residue:body#".
1659
1660    If four positional arguments are supplied, they are:
1661
1662    :param str/int phasenum: The number for the phase (or None or '*')
1663    :param str/int histnum: The number for the histogram (or None or '*')
1664    :param str varname: a single value can be used to create a :class:`G2VarObj`
1665    :param str/int atomnum: The number for the atom (or None or '*')
1666
1667    '''
1668    IDdict = {}
1669    IDdict['phases'] = {}
1670    IDdict['hists'] = {}
1671    IDdict['atoms'] = {}
1672    def __init__(self,*args):
1673        self.phase = None
1674        self.histogram = None
1675        self.name = ''
1676        self.atom = None
1677        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
1678            # single arg with 4 values
1679            self.phase,self.histogram,self.name,self.atom = args[0]
1680        elif len(args) == 1 and ':' in args[0]:
1681            #parse a string
1682            lst = args[0].split(':')
1683            if lst[0] == '*':
1684                self.phase = '*'
1685                if len(lst) > 3:
1686                    self.atom = lst[3]
1687                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1688            elif lst[1] == '*':
1689                self.histogram = '*'
1690                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1691            else:
1692                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1693                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1694                if len(lst) == 4:
1695                    if lst[3] == '*':
1696                        self.atom = '*'
1697                    else:
1698                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
1699                elif len(lst) == 5:
1700                    self.atom = lst[3]+":"+lst[4]
1701                elif len(lst) == 3:
1702                    pass
1703                else:
1704                    raise Exception,"Too many colons in var name "+str(args[0])
1705            self.name = lst[2]
1706        elif len(args) == 4:
1707            if args[0] == '*':
1708                self.phase = '*'
1709                self.atom = args[3]
1710            else:
1711                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
1712                if args[3] == '*':
1713                    self.atom = '*'
1714                elif args[0] is not None:
1715                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
1716            if args[1] == '*':
1717                self.histogram = '*'
1718            else:
1719                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
1720            self.name = args[2]
1721        else:
1722            raise Exception,"Incorrectly called GSAS-II parameter name"
1723
1724        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
1725
1726    def __str__(self):
1727        return self.varname()
1728
1729    def varname(self):
1730        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
1731        string (p:h:<var>:a) or (p:h:<var>)
1732
1733        :returns: the variable name as a str
1734        '''
1735        a = ""
1736        if self.phase == "*":
1737            ph = "*"
1738            if self.atom:
1739                a = ":" + str(self.atom)
1740        else:
1741            ph = _lookup(PhaseRanIdLookup,self.phase)
1742            if self.atom == '*':
1743                a = ':*'
1744            elif self.atom:
1745                if ":" in str(self.atom):
1746                    a = ":" + str(self.atom)
1747                elif ph in AtomRanIdLookup:
1748                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
1749                else:
1750                    a = ":?"
1751        if self.histogram == "*":
1752            hist = "*"
1753        else:
1754            hist = _lookup(HistRanIdLookup,self.histogram)
1755        s = (ph + ":" + hist + ":" + str(self.name)) + a
1756        return s
1757
1758    def __repr__(self):
1759        '''Return the detailed contents of the object
1760        '''
1761        s = "<"
1762        if self.phase == '*':
1763            s += "Phases: all; "
1764            if self.atom is not None:
1765                if ":" in str(self.atom):
1766                    s += "Rigid body" + str(self.atom) + "; "
1767                else:
1768                    s += "Atom #" + str(self.atom) + "; "
1769        elif self.phase is not None:
1770            ph =  _lookup(PhaseRanIdLookup,self.phase)
1771            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
1772            if self.atom == '*':
1773                s += "Atoms: all; "
1774            elif ":" in str(self.atom):
1775                s += "Rigid body" + str(self.atom) + "; "
1776            elif self.atom is not None:
1777                s += "Atom rId=" + str(self.atom)
1778                if ph in AtomRanIdLookup:
1779                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
1780                else:
1781                    s += " (#? -- not found!); "
1782        if self.histogram == '*':
1783            s += "Histograms: all; "
1784        elif self.histogram is not None:
1785            hist = _lookup(HistRanIdLookup,self.histogram)
1786            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
1787        s += 'Variable name="' + str(self.name) + '">'
1788        return s+" ("+self.varname()+")"
1789
1790    def __eq__(self, other):
1791        if type(other) is type(self):
1792            return (self.phase == other.phase and
1793                    self.histogram == other.histogram and
1794                    self.name == other.name and
1795                    self.atom == other.atom)
1796        return False
1797
1798    def _show(self):
1799        'For testing, shows the current lookup table'
1800        print 'phases', self.IDdict['phases']
1801        print 'hists', self.IDdict['hists']
1802        print 'atomDict', self.IDdict['atoms']
1803
1804#==========================================================================
1805def SetDefaultSample():
1806    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
1807    return {
1808        'InstrName':'',
1809        'ranId':ran.randint(0,sys.maxint),
1810        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
1811        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],'Diffuse':[],
1812        'Temperature':300.,'Pressure':0.1,'Time':0.0,
1813        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
1814        'Gonio. radius':200.0,
1815        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
1816#SASD items
1817        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
1818        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
1819        'Trans':1.0,                            #measured transmission
1820        'SlitLen':0.0,                          #Slit length - in Q(A-1)
1821        }
1822######################################################################
1823class ImportBaseclass(object):
1824    '''Defines a base class for the reading of input files (diffraction
1825    data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1826    for an explanation on how to use a subclass of this class.
1827    '''
1828    class ImportException(Exception):
1829        '''Defines an Exception that is used when an import routine hits an expected error,
1830        usually in .Reader.
1831
1832        Good practice is that the Reader should define a value in self.errors that
1833        tells the user some information about what is wrong with their file.
1834        '''
1835        pass
1836
1837    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
1838    def __init__(self,formatName,longFormatName=None,
1839                 extensionlist=[],strictExtension=False,):
1840        self.formatName = formatName # short string naming file type
1841        if longFormatName: # longer string naming file type
1842            self.longFormatName = longFormatName
1843        else:
1844            self.longFormatName = formatName
1845        # define extensions that are allowed for the file type
1846        # for windows, remove any extensions that are duplicate, as case is ignored
1847        if sys.platform == 'windows' and extensionlist:
1848            extensionlist = list(set([s.lower() for s in extensionlist]))
1849        self.extensionlist = extensionlist
1850        # If strictExtension is True, the file will not be read, unless
1851        # the extension matches one in the extensionlist
1852        self.strictExtension = strictExtension
1853        self.errors = ''
1854        self.warnings = ''
1855        self.SciPy = False          #image reader needed scipy
1856        # used for readers that will use multiple passes to read
1857        # more than one data block
1858        self.repeat = False
1859        self.selections = []
1860        self.repeatcount = 0
1861        self.readfilename = '?'
1862        self.scriptable = False
1863        #print 'created',self.__class__
1864
1865    def ReInitialize(self):
1866        'Reinitialize the Reader to initial settings'
1867        self.errors = ''
1868        self.warnings = ''
1869        self.SciPy = False          #image reader needed scipy
1870        self.repeat = False
1871        self.repeatcount = 0
1872        self.readfilename = '?'
1873
1874
1875#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1876#        '''This method must be supplied in the child class to read the file.
1877#        if the read fails either return False or raise an Exception
1878#        preferably of type ImportException.
1879#        '''
1880#        #start reading
1881#        raise ImportException("Error occurred while...")
1882#        self.errors += "Hint for user on why the error occur
1883#        return False # if an error occurs
1884#        return True # if read OK
1885
1886    def ExtensionValidator(self, filename):
1887        '''This methods checks if the file has the correct extension
1888        Return False if this filename will not be supported by this reader
1889        Return True if the extension matches the list supplied by the reader
1890        Return None if the reader allows un-registered extensions
1891        '''
1892        if filename:
1893            ext = ospath.splitext(filename)[1]
1894            if sys.platform == 'windows': ext = ext.lower()
1895            if ext in self.extensionlist: return True
1896            if self.strictExtension: return False
1897        return None
1898
1899    def ContentsValidator(self, filepointer):
1900        '''This routine will attempt to determine if the file can be read
1901        with the current format.
1902        This will typically be overridden with a method that
1903        takes a quick scan of [some of]
1904        the file contents to do a "sanity" check if the file
1905        appears to match the selected format.
1906        '''
1907        #filepointer.seek(0) # rewind the file pointer
1908        return True
1909
1910    def CIFValidator(self, filepointer):
1911        '''A :meth:`ContentsValidator` for use to validate CIF files.
1912        '''
1913        for i,l in enumerate(filepointer):
1914            if i >= 1000: return True
1915            '''Encountered only blank lines or comments in first 1000
1916            lines. This is unlikely, but assume it is CIF anyway, since we are
1917            even less likely to find a file with nothing but hashes and
1918            blank lines'''
1919            line = l.strip()
1920            if len(line) == 0: # ignore blank lines
1921                continue
1922            elif line.startswith('#'): # ignore comments
1923                continue
1924            elif line.startswith('data_'): # on the right track, accept this file
1925                return True
1926            else: # found something invalid
1927                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1928                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1929                    self.errors += '  '+str(l)
1930                else:
1931                    self.errors += '  (binary)'
1932                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
1933                self.errors += '\n        a data_ statement begins a block.'
1934                return False
1935
1936######################################################################
1937class ImportPhase(ImportBaseclass):
1938    '''Defines a base class for the reading of files with coordinates
1939
1940    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1941    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase`.
1942    See :ref:`Writing a Import Routine<Import_Routines>`
1943    for an explanation on how to use this class.
1944
1945    '''
1946    def __init__(self,formatName,longFormatName=None,extensionlist=[],
1947        strictExtension=False,):
1948        # call parent __init__
1949        ImportBaseclass.__init__(self,formatName,longFormatName,
1950            extensionlist,strictExtension)
1951        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1952        self.Constraints = None
1953
1954######################################################################
1955class ImportStructFactor(ImportBaseclass):
1956    '''Defines a base class for the reading of files with tables
1957    of structure factors.
1958
1959    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
1960    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
1961    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1962    :meth:`Reader`.
1963
1964    See :ref:`Writing a Import Routine<Import_Routines>`
1965    for an explanation on how to use import classes in general. The specifics
1966    for reading a structure factor histogram require that
1967    the ``Reader()`` routine in the import
1968    class need to do only a few things: It
1969    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1970    and set :attr:`Parameters` with the instrument parameters
1971    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1972    '''
1973    def __init__(self,formatName,longFormatName=None,extensionlist=[],
1974        strictExtension=False,):
1975        ImportBaseclass.__init__(self,formatName,longFormatName,
1976            extensionlist,strictExtension)
1977
1978        # define contents of Structure Factor entry
1979        self.Parameters = []
1980        'self.Parameters is a list with two dicts for data parameter settings'
1981        self.InitParameters()
1982        self.RefDict = {'RefList':[],'FF':{},'Super':0}
1983        self.Banks = []             #for multi bank data (usually TOF)
1984        '''self.RefDict is a dict containing the reflection information, as read from the file.
1985        Item 'RefList' contains the reflection information. See the
1986        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1987        for the contents of each row. Dict element 'FF'
1988        contains the form factor values for each element type; if this entry
1989        is left as initialized (an empty list) it will be initialized as needed later.
1990        '''
1991    def ReInitialize(self):
1992        'Reinitialize the Reader to initial settings'
1993        ImportBaseclass.ReInitialize(self)
1994        self.InitParameters()
1995        self.Banks = []             #for multi bank data (usually TOF)
1996        self.RefDict = {'RefList':[],'FF':{},'Super':0}
1997
1998    def InitParameters(self):
1999        'initialize the instrument parameters structure'
2000        Lambda = 0.70926
2001        HistType = 'SXC'
2002        self.Parameters = [{'Type':[HistType,HistType], # create the structure
2003                            'Lam':[Lambda,Lambda]
2004                            }, {}]
2005        'Parameters is a list with two dicts for data parameter settings'
2006
2007    def UpdateParameters(self,Type=None,Wave=None):
2008        'Revise the instrument parameters'
2009        if Type is not None:
2010            self.Parameters[0]['Type'] = [Type,Type]
2011        if Wave is not None:
2012            self.Parameters[0]['Lam'] = [Wave,Wave]
2013
2014######################################################################
2015class ImportPowderData(ImportBaseclass):
2016    '''Defines a base class for the reading of files with powder data.
2017
2018    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
2019    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder`.
2020    See :ref:`Writing a Import Routine<Import_Routines>`
2021    for an explanation on how to use this class.
2022    '''
2023    def __init__(self,formatName,longFormatName=None,
2024        extensionlist=[],strictExtension=False,):
2025        ImportBaseclass.__init__(self,formatName,longFormatName,
2026            extensionlist,strictExtension)
2027        self.clockWd = None  # used in TOF
2028        self.ReInitialize()
2029
2030    def ReInitialize(self):
2031        'Reinitialize the Reader to initial settings'
2032        ImportBaseclass.ReInitialize(self)
2033        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
2034        self.powderdata = [] # Powder dataset
2035        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
2036                np.array(x), # x-axis values
2037                np.array(y), # powder pattern intensities
2038                np.array(w), # 1/sig(intensity)^2 values (weights)
2039                np.array(yc), # calc. intensities (zero)
2040                np.array(yb), # calc. background (zero)
2041                np.array(yd), # obs-calc profiles
2042        '''
2043        self.comments = []
2044        self.idstring = ''
2045        self.Sample = SetDefaultSample() # default sample parameters
2046        self.Controls = {}  # items to be placed in top-level Controls
2047        self.GSAS = None     # used in TOF
2048        self.repeat_instparm = True # Should a parm file be
2049        #                             used for multiple histograms?
2050        self.instparm = None # name hint from file of instparm to use
2051        self.instfile = '' # full path name to instrument parameter file
2052        self.instbank = '' # inst parm bank number
2053        self.instmsg = ''  # a label that gets printed to show
2054                           # where instrument parameters are from
2055        self.numbanks = 1
2056        self.instdict = {} # place items here that will be transferred to the instrument parameters
2057        self.pwdparms = {} # place parameters that are transferred directly to the tree
2058                           # here (typically from an existing GPX file)
2059######################################################################
2060class ImportSmallAngleData(ImportBaseclass):
2061    '''Defines a base class for the reading of files with small angle data.
2062    See :ref:`Writing a Import Routine<Import_Routines>`
2063    for an explanation on how to use this class.
2064    '''
2065    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2066        strictExtension=False,):
2067
2068        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2069            strictExtension)
2070        self.ReInitialize()
2071
2072    def ReInitialize(self):
2073        'Reinitialize the Reader to initial settings'
2074        ImportBaseclass.ReInitialize(self)
2075        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2076        self.smallangledata = [] # SASD dataset
2077        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2078                np.array(x), # x-axis values
2079                np.array(y), # powder pattern intensities
2080                np.array(w), # 1/sig(intensity)^2 values (weights)
2081                np.array(yc), # calc. intensities (zero)
2082                np.array(yd), # obs-calc profiles
2083                np.array(yb), # preset bkg
2084        '''
2085        self.comments = []
2086        self.idstring = ''
2087        self.Sample = SetDefaultSample()
2088        self.GSAS = None     # used in TOF
2089        self.clockWd = None  # used in TOF
2090        self.numbanks = 1
2091        self.instdict = {} # place items here that will be transferred to the instrument parameters
2092
2093######################################################################
2094class ImportReflectometryData(ImportBaseclass):
2095    '''Defines a base class for the reading of files with reflectometry data.
2096    See :ref:`Writing a Import Routine<Import_Routines>`
2097    for an explanation on how to use this class.
2098    '''
2099    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2100        strictExtension=False,):
2101
2102        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2103            strictExtension)
2104        self.ReInitialize()
2105
2106    def ReInitialize(self):
2107        'Reinitialize the Reader to initial settings'
2108        ImportBaseclass.ReInitialize(self)
2109        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2110        self.reflectometrydata = [] # SASD dataset
2111        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2112                np.array(x), # x-axis values
2113                np.array(y), # powder pattern intensities
2114                np.array(w), # 1/sig(intensity)^2 values (weights)
2115                np.array(yc), # calc. intensities (zero)
2116                np.array(yd), # obs-calc profiles
2117                np.array(yb), # preset bkg
2118        '''
2119        self.comments = []
2120        self.idstring = ''
2121        self.Sample = SetDefaultSample()
2122        self.GSAS = None     # used in TOF
2123        self.clockWd = None  # used in TOF
2124        self.numbanks = 1
2125        self.instdict = {} # place items here that will be transferred to the instrument parameters
2126
2127######################################################################
2128class ImportPDFData(ImportBaseclass):
2129    '''Defines a base class for the reading of files with PDF G(R) data.
2130    See :ref:`Writing a Import Routine<Import_Routines>`
2131    for an explanation on how to use this class.
2132    '''
2133    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2134        strictExtension=False,):
2135
2136        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2137            strictExtension)
2138        self.ReInitialize()
2139
2140    def ReInitialize(self):
2141        'Reinitialize the Reader to initial settings'
2142        ImportBaseclass.ReInitialize(self)
2143        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2144        self.pdfdata = [] # PDF G(R) dataset
2145        '''A pdf g(r) data set is a list with items [x,y]:
2146                np.array(x), # r-axis values
2147                np.array(y), # pdf g(r)
2148        '''
2149        self.comments = []
2150        self.idstring = ''
2151        self.numbanks = 1
2152
2153######################################################################
2154class ImportImage(ImportBaseclass):
2155    '''Defines a base class for the reading of images
2156
2157    Images are read in only these places:
2158
2159      * Initial reading is typically done from a menu item
2160        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2161        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2162        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2163        :meth:`Reader`. This returns a list of reader objects for each read image.
2164
2165      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2166        directly into the data tree.
2167
2168      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2169
2170    .. _Image_import_routines:
2171
2172    When reading an image, the ``Reader()`` routine in the ImportImage class
2173    should set:
2174
2175      * :attr:`Comments`: a list of strings (str),
2176      * :attr:`Npix`: the number of pixels in the image (int),
2177      * :attr:`Image`: the actual image as a numpy array (np.array)
2178      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2179        data items are needed:
2180
2181         * 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
2182         * 'wavelength': wavelength in Angstoms.
2183         * 'distance': distance of detector from sample in cm.
2184         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2185         * 'size': size of image (such as ``[2048,2048]``).
2186         * 'ImageTag': image number or other keyword used to retrieve image from
2187           a multi-image data file (defaults to ``1`` if not specified).
2188         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2189
2190    optional data items:
2191
2192      * :attr:`repeat`: set to True if there are additional images to
2193        read in the file, False otherwise
2194      * :attr:`repeatcount`: set to the number of the image.
2195
2196    Note that the above is initialized with :meth:`InitParameters`.
2197    (Also see :ref:`Writing a Import Routine<Import_Routines>`
2198    for an explanation on how to use import classes in general.)
2199    '''
2200    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2201        strictExtension=False,):
2202        ImportBaseclass.__init__(self,formatName,longFormatName,
2203            extensionlist,strictExtension)
2204        self.InitParameters()
2205
2206    def ReInitialize(self):
2207        'Reinitialize the Reader to initial settings -- not used at present'
2208        ImportBaseclass.ReInitialize(self)
2209        self.InitParameters()
2210
2211    def InitParameters(self):
2212        'initialize the instrument parameters structure'
2213        self.Comments = ['No comments']
2214        self.Data = {}
2215        self.Npix = 0
2216        self.Image = None
2217        self.repeat = False
2218        self.repeatcount = 1
2219        self.sumfile = ''
2220
2221    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2222        '''Optionally, call this after reading in an image to load it into the tree.
2223        This saves time by preventing a reread of the same information.
2224        '''
2225        if ParentFrame:
2226            ParentFrame.ImageZ = self.Image   # store the image for plotting
2227            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2228            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read
2229
2230#################################################################################################
2231# shortcut routines
2232exp = np.exp
2233sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2234cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2235tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2236sqrt = sq = lambda x: np.sqrt(x)
2237pi = lambda: np.pi
2238class ExpressionObj(object):
2239    '''Defines an object with a user-defined expression, to be used for
2240    secondary fits or restraints. Object is created null, but is changed
2241    using :meth:`LoadExpression`. This contains only the minimum
2242    information that needs to be stored to save and load the expression
2243    and how it is mapped to GSAS-II variables.
2244    '''
2245    def __init__(self):
2246        self.expression = ''
2247        'The expression as a text string'
2248        self.assgnVars = {}
2249        '''A dict where keys are label names in the expression mapping to a GSAS-II
2250        variable. The value a G2 variable name.
2251        Note that the G2 variable name may contain a wild-card and correspond to
2252        multiple values.
2253        '''
2254        self.freeVars = {}
2255        '''A dict where keys are label names in the expression mapping to a free
2256        parameter. The value is a list with:
2257
2258         * a name assigned to the parameter
2259         * a value for to the parameter and
2260         * a flag to determine if the variable is refined.
2261        '''
2262        self.depVar = None
2263
2264        self.lastError = ('','')
2265        '''Shows last encountered error in processing expression
2266        (list of 1-3 str values)'''
2267
2268        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2269        self.distance_atoms = None  # to be used for defining atom distances
2270
2271    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2272        '''Load the expression and associated settings into the object. Raises
2273        an exception if the expression is not parsed, if not all functions
2274        are defined or if not all needed parameter labels in the expression
2275        are defined.
2276
2277        This will not test if the variable referenced in these definitions
2278        are actually in the parameter dictionary. This is checked when the
2279        computation for the expression is done in :meth:`SetupCalc`.
2280
2281        :param str expr: the expression
2282        :param list exprVarLst: parameter labels found in the expression
2283        :param dict varSelect: this will be 0 for Free parameters
2284          and non-zero for expression labels linked to G2 variables.
2285        :param dict varName: Defines a name (str) associated with each free parameter
2286        :param dict varValue: Defines a value (float) associated with each free parameter
2287        :param dict varRefflag: Defines a refinement flag (bool)
2288          associated with each free parameter
2289        '''
2290        self.expression = expr
2291        self.compiledExpr = None
2292        self.freeVars = {}
2293        self.assgnVars = {}
2294        for v in exprVarLst:
2295            if varSelect[v] == 0:
2296                self.freeVars[v] = [
2297                    varName.get(v),
2298                    varValue.get(v),
2299                    varRefflag.get(v),
2300                    ]
2301            else:
2302                self.assgnVars[v] = varName[v]
2303        self.CheckVars()
2304
2305    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2306        '''Load the expression and associated settings from the object into
2307        arrays used for editing.
2308
2309        :param list exprVarLst: parameter labels found in the expression
2310        :param dict varSelect: this will be 0 for Free parameters
2311          and non-zero for expression labels linked to G2 variables.
2312        :param dict varName: Defines a name (str) associated with each free parameter
2313        :param dict varValue: Defines a value (float) associated with each free parameter
2314        :param dict varRefflag: Defines a refinement flag (bool)
2315          associated with each free parameter
2316
2317        :returns: the expression as a str
2318        '''
2319        for v in self.freeVars:
2320            varSelect[v] = 0
2321            varName[v] = self.freeVars[v][0]
2322            varValue[v] = self.freeVars[v][1]
2323            varRefflag[v] = self.freeVars[v][2]
2324        for v in self.assgnVars:
2325            varSelect[v] = 1
2326            varName[v] = self.assgnVars[v]
2327        return self.expression
2328
2329    def GetVaried(self):
2330        'Returns the names of the free parameters that will be refined'
2331        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
2332
2333    def GetVariedVarVal(self):
2334        'Returns the names and values of the free parameters that will be refined'
2335        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
2336
2337    def UpdateVariedVars(self,varyList,values):
2338        'Updates values for the free parameters (after a refinement); only updates refined vars'
2339        for v in self.freeVars:
2340            if not self.freeVars[v][2]: continue
2341            if "::"+self.freeVars[v][0] not in varyList: continue
2342            indx = varyList.index("::"+self.freeVars[v][0])
2343            self.freeVars[v][1] = values[indx]
2344
2345    def GetIndependentVars(self):
2346        'Returns the names of the required independent parameters used in expression'
2347        return [self.assgnVars[v] for v in self.assgnVars]
2348
2349    def CheckVars(self):
2350        '''Check that the expression can be parsed, all functions are
2351        defined and that input loaded into the object is internally
2352        consistent. If not an Exception is raised.
2353
2354        :returns: a dict with references to packages needed to
2355          find functions referenced in the expression.
2356        '''
2357        ret = self.ParseExpression(self.expression)
2358        if not ret:
2359            raise Exception("Expression parse error")
2360        exprLblList,fxnpkgdict = ret
2361        # check each var used in expression is defined
2362        defined = self.assgnVars.keys() + self.freeVars.keys()
2363        notfound = []
2364        for var in exprLblList:
2365            if var not in defined:
2366                notfound.append(var)
2367        if notfound:
2368            msg = 'Not all variables defined'
2369            msg1 = 'The following variables were not defined: '
2370            msg2 = ''
2371            for var in notfound:
2372                if msg: msg += ', '
2373                msg += var
2374            self.lastError = (msg1,'  '+msg2)
2375            raise Exception(msg)
2376        return fxnpkgdict
2377
2378    def ParseExpression(self,expr):
2379        '''Parse an expression and return a dict of called functions and
2380        the variables used in the expression. Returns None in case an error
2381        is encountered. If packages are referenced in functions, they are loaded
2382        and the functions are looked up into the modules global
2383        workspace.
2384
2385        Note that no changes are made to the object other than
2386        saving an error message, so that this can be used for testing prior
2387        to the save.
2388
2389        :returns: a list of used variables
2390        '''
2391        self.lastError = ('','')
2392        import ast
2393        def FindFunction(f):
2394            '''Find the object corresponding to function f
2395            :param str f: a function name such as 'numpy.exp'
2396            :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2397              that defines the package location(s) and where pkgobj
2398              defines the object associated with the function.
2399              If the function is not found, pkgobj is None.
2400            '''
2401            df = f.split('.')
2402            pkgdict = {}
2403            # no listed package, try in current namespace
2404            if len(df) == 1:
2405                try:
2406                    fxnobj = eval(f)
2407                    return pkgdict,fxnobj
2408                except (AttributeError, NameError):
2409                    return None,None
2410            else:
2411                try:
2412                    fxnobj = eval(f)
2413                    pkgdict[df[0]] = eval(df[0])
2414                    return pkgdict,fxnobj
2415                except (AttributeError, NameError):
2416                    pass
2417            # includes a package, lets try to load the packages
2418            pkgname = ''
2419            path = sys.path+['./',]
2420            for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2421                if pkgname:
2422                    pkgname += '.' + pkg
2423                else:
2424                    pkgname = pkg
2425                fp = None
2426                try:
2427                    fp, fppath,desc = imp.find_module(pkg,path)
2428                    pkgobj = imp.load_module(pkg,fp,fppath,desc)
2429                    pkgdict[pkgname] = pkgobj
2430                    path = [fppath]
2431                except Exception as msg:
2432                    print('load of '+pkgname+' failed with error='+str(msg))
2433                    return {},None
2434                finally:
2435                    if fp: fp.close()
2436                try:
2437                    #print 'before',pkgdict.keys()
2438                    fxnobj = eval(f,globals(),pkgdict)
2439                    #print 'after 1',pkgdict.keys()
2440                    #fxnobj = eval(f,pkgdict)
2441                    #print 'after 2',pkgdict.keys()
2442                    return pkgdict,fxnobj
2443                except:
2444                    continue
2445            return None # not found
2446        def ASTtransverse(node,fxn=False):
2447            '''Transverse a AST-parsed expresson, compiling a list of variables
2448            referenced in the expression. This routine is used recursively.
2449
2450            :returns: varlist,fxnlist where
2451              varlist is a list of referenced variable names and
2452              fxnlist is a list of used functions
2453            '''
2454            varlist = []
2455            fxnlist = []
2456            if isinstance(node, list):
2457                for b in node:
2458                    v,f = ASTtransverse(b,fxn)
2459                    varlist += v
2460                    fxnlist += f
2461            elif isinstance(node, ast.AST):
2462                for a, b in ast.iter_fields(node):
2463                    if isinstance(b, ast.AST):
2464                        if a == 'func':
2465                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
2466                            continue
2467                        v,f = ASTtransverse(b,fxn)
2468                        varlist += v
2469                        fxnlist += f
2470                    elif isinstance(b, list):
2471                        v,f = ASTtransverse(b,fxn)
2472                        varlist += v
2473                        fxnlist += f
2474                    elif node.__class__.__name__ == "Name":
2475                        varlist += [b]
2476                    elif fxn and node.__class__.__name__ == "Attribute":
2477                        varlist += [b]
2478            return varlist,fxnlist
2479        try:
2480            exprast = ast.parse(expr)
2481        except SyntaxError:
2482            s = ''
2483            import traceback
2484            for i in traceback.format_exc().splitlines()[-3:-1]:
2485                if s: s += "\n"
2486                s += str(i)
2487            self.lastError = ("Error parsing expression:",s)
2488            return
2489        # find the variables & functions
2490        v,f = ASTtransverse(exprast)
2491        varlist = sorted(list(set(v)))
2492        fxnlist = list(set(f))
2493        pkgdict = {}
2494        # check the functions are defined
2495        for fxn in fxnlist:
2496            fxndict,fxnobj = FindFunction(fxn)
2497            if not fxnobj:
2498                self.lastError = ("Error: Invalid function",fxn,
2499                                  "is not defined")
2500                return
2501            if not hasattr(fxnobj,'__call__'):
2502                self.lastError = ("Error: Not a function.",fxn,
2503                                  "cannot be called as a function")
2504                return
2505            pkgdict.update(fxndict)
2506        return varlist,pkgdict
2507
2508    def GetDepVar(self):
2509        'return the dependent variable, or None'
2510        return self.depVar
2511
2512    def SetDepVar(self,var):
2513        'Set the dependent variable, if used'
2514        self.depVar = var
2515#==========================================================================
2516class ExpressionCalcObj(object):
2517    '''An object used to evaluate an expression from a :class:`ExpressionObj`
2518    object.
2519
2520    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
2521      an expression string and mappings for the parameter labels in that object.
2522    '''
2523    def __init__(self,exprObj):
2524        self.eObj = exprObj
2525        'The expression and mappings; a :class:`ExpressionObj` object'
2526        self.compiledExpr = None
2527        'The expression as compiled byte-code'
2528        self.exprDict = {}
2529        '''dict that defines values for labels used in expression and packages
2530        referenced by functions
2531        '''
2532        self.lblLookup = {}
2533        '''Lookup table that specifies the expression label name that is
2534        tied to a particular GSAS-II parameters in the parmDict.
2535        '''
2536        self.fxnpkgdict = {}
2537        '''a dict with references to packages needed to
2538        find functions referenced in the expression.
2539        '''
2540        self.varLookup = {}
2541        '''Lookup table that specifies the GSAS-II variable(s)
2542        indexed by the expression label name. (Used for only for diagnostics
2543        not evaluation of expression.)
2544        '''
2545        self.su = None
2546        '''Standard error evaluation where supplied by the evaluator
2547        '''
2548        # Patch: for old-style expressions with a (now removed step size)
2549        for v in self.eObj.assgnVars:
2550            if not isinstance(self.eObj.assgnVars[v], basestring):
2551                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
2552        self.parmDict = {}
2553        '''A copy of the parameter dictionary, for distance and angle computation
2554        '''
2555
2556    def SetupCalc(self,parmDict):
2557        '''Do all preparations to use the expression for computation.
2558        Adds the free parameter values to the parameter dict (parmDict).
2559        '''
2560        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2561            return
2562        self.fxnpkgdict = self.eObj.CheckVars()
2563        # all is OK, compile the expression
2564        self.compiledExpr = compile(self.eObj.expression,'','eval')
2565
2566        # look at first value in parmDict to determine its type
2567        parmsInList = True
2568        for key in parmDict:
2569            val = parmDict[key]
2570            if isinstance(val, basestring):
2571                parmsInList = False
2572                break
2573            try: # check if values are in lists
2574                val = parmDict[key][0]
2575            except (TypeError,IndexError):
2576                parmsInList = False
2577            break
2578
2579        # set up the dicts needed to speed computations
2580        self.exprDict = {}
2581        self.lblLookup = {}
2582        self.varLookup = {}
2583        for v in self.eObj.freeVars:
2584            varname = self.eObj.freeVars[v][0]
2585            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
2586            self.lblLookup[varname] = v
2587            self.varLookup[v] = varname
2588            if parmsInList:
2589                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
2590            else:
2591                parmDict[varname] = self.eObj.freeVars[v][1]
2592            self.exprDict[v] = self.eObj.freeVars[v][1]
2593        for v in self.eObj.assgnVars:
2594            varname = self.eObj.assgnVars[v]
2595            if '*' in varname:
2596                varlist = LookupWildCard(varname,parmDict.keys())
2597                if len(varlist) == 0:
2598                    raise Exception,"No variables match "+str(v)
2599                for var in varlist:
2600                    self.lblLookup[var] = v
2601                if parmsInList:
2602                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
2603                else:
2604                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
2605                self.varLookup[v] = [var for var in varlist]
2606            elif varname in parmDict:
2607                self.lblLookup[varname] = v
2608                self.varLookup[v] = varname
2609                if parmsInList:
2610                    self.exprDict[v] = parmDict[varname][0]
2611                else:
2612                    self.exprDict[v] = parmDict[varname]
2613            else:
2614                self.exprDict[v] = None
2615#                raise Exception,"No value for variable "+str(v)
2616        self.exprDict.update(self.fxnpkgdict)
2617
2618    def UpdateVars(self,varList,valList):
2619        '''Update the dict for the expression with a set of values
2620        :param list varList: a list of variable names
2621        :param list valList: a list of corresponding values
2622        '''
2623        for var,val in zip(varList,valList):
2624            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
2625
2626    def UpdateDict(self,parmDict):
2627        '''Update the dict for the expression with values in a dict
2628        :param list parmDict: a dict of values some of which may be in use here
2629        '''
2630        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2631            self.parmDict = parmDict
2632            return
2633        for var in parmDict:
2634            if var in self.lblLookup:
2635                self.exprDict[self.lblLookup[var]] = parmDict[var]
2636
2637    def EvalExpression(self):
2638        '''Evaluate an expression. Note that the expression
2639        and mapping are taken from the :class:`ExpressionObj` expression object
2640        and the parameter values were specified in :meth:`SetupCalc`.
2641        :returns: a single value for the expression. If parameter
2642        values are arrays (for example, from wild-carded variable names),
2643        the sum of the resulting expression is returned.
2644
2645        For example, if the expression is ``'A*B'``,
2646        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
2647
2648        [0.5, 1, 0.5]
2649
2650        then the result will be ``4.0``.
2651        '''
2652        self.su = None
2653        if self.eObj.expression.startswith('Dist'):
2654#            GSASIIpath.IPyBreak()
2655            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
2656            return dist
2657        elif self.eObj.expression.startswith('Angle'):
2658            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
2659            return angle
2660        if self.compiledExpr is None:
2661            raise Exception,"EvalExpression called before SetupCalc"
2662        try:
2663            val = eval(self.compiledExpr,globals(),self.exprDict)
2664        except TypeError:
2665            val = None
2666        if not np.isscalar(val):
2667            val = np.sum(val)
2668        return val
2669
2670class G2Exception(Exception):
2671    def __init__(self,msg):
2672        self.msg = msg
2673    def __str__(self):
2674        return repr(self.msg)
2675
2676def HowDidIgetHere(wherecalledonly=False):
2677    '''Show a traceback with calls that brought us to the current location.
2678    Used for debugging.
2679    '''
2680    import traceback
2681    if wherecalledonly:
2682        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
2683        print(i.strip().rstrip())
2684    else:
2685        print 70*'*'
2686        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
2687        print 70*'*'
2688
2689def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
2690    '''Create and initialize a new set of PDF tree entries
2691
2692    :param Frame G2frame: main GSAS-II tree frame object
2693    :param str PWDRtree: name of PWDR to be used to create PDF item
2694    :param dict ElList: data structure with composition
2695    :param list Qlimits: Q limits to be used for computing the PDF
2696    :param float numAtm: no. atom in chemical formula
2697    :param float FltBkg: flat background value
2698    :param list PDFnames: previously used PDF names
2699
2700    :returns: the Id of the newly created PDF entry
2701    '''
2702    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
2703    if PDFname in PDFnames:
2704        print('Skipping, entry already exists: '+PDFname)
2705        return None
2706    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
2707    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
2708    Data = {
2709        'Sample':{'Name':PWDRtree,'Mult':1.0},
2710        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
2711        'Container':{'Name':'','Mult':-1.0,'Refine':False},
2712        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
2713        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
2714        'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
2715        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,
2716        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
2717    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
2718    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
2719        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
2720    return Id
2721
2722class ShowTiming(object):
2723    '''An object to use for timing repeated sections of code.
2724
2725    Create the object with::
2726       tim0 = ShowTiming()
2727
2728    Tag sections of code to be timed with::
2729       tim0.start('start')
2730       tim0.start('in section 1')
2731       tim0.start('in section 2')
2732    etc. (Note that each section should have a unique label.)
2733
2734    After the last section, end timing with::
2735       tim0.end()
2736
2737    Show timing results with::
2738       tim0.show()
2739       
2740    '''
2741    def __init__(self):
2742        self.timeSum =  []
2743        self.timeStart = []
2744        self.label = []
2745        self.prev = None
2746    def start(self,label):
2747        if label in self.label:
2748            i = self.label.index(label)
2749            self.timeStart[i] = time.time()
2750        else:
2751            i = len(self.label)
2752            self.timeSum.append(0.0)
2753            self.timeStart.append(time.time())
2754            self.label.append(label)
2755        if self.prev is not None:
2756            self.timeSum[self.prev] += self.timeStart[i] - self.timeStart[self.prev]
2757        self.prev = i
2758    def end(self):
2759        if self.prev is not None:
2760            self.timeSum[self.prev] += time.time() - self.timeStart[self.prev]
2761        self.prev = None
2762    def show(self):
2763        sumT = sum(self.timeSum)
2764        print('Timing results (total={:.2f} sec)'.format(sumT))
2765        for i,(lbl,val) in enumerate(zip(self.label,self.timeSum)):
2766            print('{} {:20} {:8.2f} ms {:5.2f}%'.format(i,lbl,1000.*val,100*val/sumT))
2767
2768
2769if __name__ == "__main__":
2770    # test equation evaluation
2771    def showEQ(calcobj):
2772        print 50*'='
2773        print calcobj.eObj.expression,'=',calcobj.EvalExpression()
2774        for v in sorted(calcobj.varLookup):
2775            print "  ",v,'=',calcobj.exprDict[v],'=',calcobj.varLookup[v]
2776        # print '  Derivatives'
2777        # for v in calcobj.derivStep.keys():
2778        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
2779
2780    obj = ExpressionObj()
2781
2782    obj.expression = "A*np.exp(B)"
2783    obj.assgnVars =  {'B': '0::Afrac:1'}
2784    obj.freeVars =  {'A': [u'A', 0.5, True]}
2785    #obj.CheckVars()
2786    calcobj = ExpressionCalcObj(obj)
2787
2788    obj1 = ExpressionObj()
2789    obj1.expression = "A*np.exp(B)"
2790    obj1.assgnVars =  {'B': '0::Afrac:*'}
2791    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
2792    #obj.CheckVars()
2793    calcobj1 = ExpressionCalcObj(obj1)
2794
2795    obj2 = ExpressionObj()
2796    obj2.distance_stuff = np.array([[0,1],[1,-1]])
2797    obj2.expression = "Dist(1,2)"
2798    GSASIIpath.InvokeDebugOpts()
2799    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
2800    calcobj2 = ExpressionCalcObj(obj2)
2801    calcobj2.SetupCalc(parmDict2)
2802    showEQ(calcobj2)
2803
2804    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
2805    print '\nDict = ',parmDict1
2806    calcobj.SetupCalc(parmDict1)
2807    showEQ(calcobj)
2808    calcobj1.SetupCalc(parmDict1)
2809    showEQ(calcobj1)
2810
2811    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
2812    print 'Dict = ',parmDict2
2813    calcobj.SetupCalc(parmDict2)
2814    showEQ(calcobj)
2815    calcobj1.SetupCalc(parmDict2)
2816    showEQ(calcobj1)
2817    calcobj2.SetupCalc(parmDict2)
2818    showEQ(calcobj2)
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