source: branch/2frame/GSASIIobj.py @ 2927

Last change on this file since 2927 was 2927, checked in by vondreele, 5 years ago

set up a local version of basinhopping.py in MCSA routine
implement frame position saving - NB: doesn't check if frame outside screen!
fix display of image controls after calibrate/recalibrate, etc.
occupancy --> site fraction in Afrac display
replace a bunch of TextCtrls? with ValidatedTxtCtrls? in phaseGUI

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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2017-07-11 21:29:11 +0000 (Tue, 11 Jul 2017) $
5# $Author: vondreele $
6# $Revision: 2927 $
7# $URL: branch/2frame/GSASIIobj.py $
8# $Id: GSASIIobj.py 2927 2017-07-11 21:29:11Z 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. (dict)
259MCSA            \            Monte-Carlo simulated annealing parameters (dict)
260\           
261==========  ===============  ====================================================
262
263Rigid Body Objects
264------------------
265
266.. _RBData_table:
267
268.. index::
269   single: Rigid Body Data description
270   single: Data object descriptions; Rigid Body Data
271   
272Rigid body descriptions are available for two types of rigid bodies: 'Vector'
273and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
274with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
275with defined refinable torsion angles.
276
277.. tabularcolumns:: |l|l|p{4in}|
278
279==========  ===============  ====================================================
280  key         sub-key        explanation
281==========  ===============  ====================================================
282Vector      RBId             vector rigid bodies (dict of dict)
283\           AtInfo           Drad, Color: atom drawing radius & color for each atom type (dict)
284\           RBname           Name assigned by user to rigid body (str)
285\           VectMag          vector magnitudes in A (list)
286\           rbXYZ            Cartesian coordinates for Vector rigid body (list of 3 float)
287\           rbRef            3 assigned reference atom nos. in rigid body for origin
288                             definition, use center of atoms flag (list of 3 int & 1 bool)
289\           VectRef          refinement flags for VectMag values (list of bool)
290\           rbTypes          Atom types for each atom in rigid body (list of str)
291\           rbVect           Cartesian vectors for each translation used to build rigid body (list of lists)
292\           useCount         Number of times rigid body is used in any structure (int)
293Residue     RBId             residue rigid bodies (dict of dict)
294\           AtInfo           Drad, Color: atom drawing radius & color for each atom type(dict)
295\           RBname           Name assigned by user to rigid body (str)
296\           rbXYZ            Cartesian coordinates for Residue rigid body (list of 3 float)
297\           rbTypes          Atom types for each atom in rigid body (list of str)
298\           atNames          Names of each atom in rigid body (e.g. C1,N2...) (list of str)
299\           rbRef            3 assigned reference atom nos. in rigid body for origin
300                             definition, use center of atoms flag (list of 3 int & 1 bool)
301\           rbSeq            Orig,Piv,angle,Riding (list): definition of internal rigid body
302                             torsion; origin atom (int), pivot atom (int), torsion angle (float),
303                             riding atoms (list of int)
304\           SelSeq           [int,int] used by SeqSizer to identify objects
305\           useCount         Number of times rigid body is used in any structure (int)
306RBIds           \            unique Ids generated upon creation of each rigid body (dict)
307\           Vector           Ids for each Vector rigid body (list)
308\           Residue          Ids for each Residue rigid body (list)
309==========  ===============  ====================================================
310
311Space Group Objects
312-------------------
313
314.. _SGData_table:
315
316.. index::
317   single: Space Group Data description
318   single: Data object descriptions; Space Group Data
319
320Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
321and the information is placed in a SGdata object
322which is a dict with these keys:
323
324.. tabularcolumns:: |l|p{4.5in}|
325
326==========  ====================================================
327  key         explanation
328==========  ====================================================
329SpGrp       space group symbol (str)
330Laue        one of the following 14 Laue classes:
331            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
332            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
333SGInv       True if centrosymmetric, False if not (bool)
334SGLatt      Lattice centering type. Will be one of
335            P, A, B, C, I, F, R (str)
336SGUniq      unique axis if monoclinic. Will be
337            a, b, or c for monoclinic space groups.
338            Will be blank for non-monoclinic. (str)
339SGCen       Symmetry cell centering vectors. A (n,3) np.array
340            of centers. Will always have at least one row:
341            ``np.array([[0, 0, 0]])``
342SGOps       symmetry operations as a list of form
343            ``[[M1,T1], [M2,T2],...]``
344            where :math:`M_n` is a 3x3 np.array
345            and :math:`T_n` is a length 3 np.array.
346            Atom coordinates are transformed where the
347            Asymmetric unit coordinates [X is (x,y,z)]
348            are transformed using
349            :math:`X^\prime = M_n*X+T_n`
350SGSys       symmetry unit cell: type one of
351            'triclinic', 'monoclinic', 'orthorhombic',
352            'tetragonal', 'rhombohedral', 'trigonal',
353            'hexagonal', 'cubic' (str)
354SGPolax     Axes for space group polarity. Will be one of
355            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
356            'xyz'. In the case where axes are arbitrary
357            '111' is used (P 1, and ?).
358==========  ====================================================
359
360.. _SSGData_table:
361
362.. index::
363   single: Superspace Group Data description
364   single: Data object descriptions; Superspace Group Data
365
366Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
367and the information is placed in a SSGdata object
368which is a dict with these keys:
369
370.. tabularcolumns:: |l|p{4.5in}|
371
372==========  ====================================================
373  key         explanation
374==========  ====================================================
375SSpGrp      superspace group symbol extension to space group
376            symbol, accidental spaces removed
377SSGCen      4D cell centering vectors [0,0,0,0] at least
378SSGOps      4D symmetry operations as [M,T] so that M*x+T = x'
379==========  ====================================================
380
381
382Atom Records
383------------
384
385.. _Atoms_table:
386
387.. index::
388   single: Atoms record description
389   single: Data object descriptions; Atoms record
390
391
392If ``phasedict`` points to the phase information in the data tree, then
393atoms are contained in a list of atom records (list) in
394``phasedict['Atoms']``. Also needed to read atom information
395are four pointers, ``cx,ct,cs,cia = phasedict['General']['atomPtrs']``,
396which define locations in the atom record, as shown below. Items shown are
397always present; additional ones for macromolecular phases are marked 'mm'
398
399.. tabularcolumns:: |l|p{4.5in}|
400
401==============   ====================================================
402location         explanation
403==============   ====================================================
404ct-4              mm - residue number (str)
405ct-3              mm - residue name (e.g. ALA) (str)
406ct-2              mm - chain label (str)
407ct-1              atom label (str)
408ct                atom type (str)
409ct+1              refinement flags; combination of 'F', 'X', 'U' (str)
410cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
411cs                site symmetry (str)
412cs+1              site multiplicity (int)
413cia               ADP flag: Isotropic ('I') or Anisotropic ('A')
414cia+1             Uiso (float)
415cia+2...cia+7     U11, U22, U33, U12, U13, U23 (6 floats)
416atom[cia+8]       unique atom identifier (int)
417
418==============   ====================================================
419
420Drawing Atom Records
421--------------------
422
423.. _Drawing_atoms_table:
424
425.. index::
426   single: Drawing atoms record description
427   single: Data object descriptions; Drawing atoms record
428
429
430If ``phasedict`` points to the phase information in the data tree, then
431drawing atoms are contained in a list of drawing atom records (list) in
432``phasedict['Drawing']['Atoms']``. Also needed to read atom information
433are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
434which define locations in the atom record, as shown below. Items shown are
435always present; additional ones for macromolecular phases are marked 'mm'
436
437.. tabularcolumns:: |l|p{4.5in}|
438
439==============   ====================================================
440location         explanation
441==============   ====================================================
442ct-4              mm - residue number (str)
443ct-3              mm - residue name (e.g. ALA) (str)
444ct-2              mm - chain label (str)
445ct-1              atom label (str)
446ct                atom type (str)
447cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
448cs-1              Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str)
449cs                atom drawing style; e.g. 'balls & sticks' (str)
450cs+1              atom label style (e.g. 'name') (str)
451cs+2              atom color (RBG triplet) (int)
452cs+3              ADP flag: Isotropic ('I') or Anisotropic ('A')
453cs+4              Uiso (float)
454cs+5...cs+11      U11, U22, U33, U12, U13, U23 (6 floats)
455ci                unique atom identifier; matches source atom Id in Atom Records (int)
456==============   ====================================================
457
458Powder Diffraction Tree Items
459-----------------------------
460
461.. _Powder_table:
462
463.. index::
464   single: Powder data object description
465   single: Data object descriptions; Powder Data
466
467Every powder diffraction histogram is stored in the GSAS-II data tree
468with a top-level entry named beginning with the string "PWDR ". The
469diffraction data for that information are directly associated with
470that tree item and there are a series of children to that item. The
471routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
472and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
473load this information into a dictionary where the child tree name is
474used as a key, and the information in the main entry is assigned
475a key of ``Data``, as outlined below.
476
477.. tabularcolumns:: |p{1in}|p{1in}|p{4in}|
478
479======================  ===============  ====================================================
480  key                      sub-key        explanation
481======================  ===============  ====================================================
482Comments                      \           Text strings extracted from the original powder
483                                          data header. These cannot be changed by the user;
484                                          it may be empty.
485Limits                       \            A list of two two element lists, as [[Ld,Hd],[L,H]]
486                                          where L and Ld are the current and default lowest
487                                          two-theta value to be used and
488                                          where H and Hd are the current and default highest
489                                          two-theta value to be used.
490Reflection Lists              \           A dict with an entry for each phase in the
491                                          histogram. The contents of each dict item
492                                          is a dict containing reflections, as described in
493                                          the :ref:`Powder Reflections <PowderRefl_table>`
494                                          description.
495Instrument Parameters         \           A list containing two dicts where the possible
496                                          keys in each dict are listed below. The value
497                                          for each item is a list containing three values:
498                                          the initial value, the current value and a
499                                          refinement flag which can have a value of
500                                          True, False or 0 where 0 indicates a value that
501                                          cannot be refined. The first and second
502                                          values are floats unless otherwise noted.
503                                          Items in the first dict are noted as [1]
504\                         Lam             Specifies a wavelength in Angstroms [1]
505\                         Lam1            Specifies the primary wavelength in
506                                          Angstrom, when an alpha1, alpha2
507                                          source is used [1]
508\                         Lam2            Specifies the secondary wavelength in
509                                          Angstrom, when an alpha1, alpha2
510                                          source is used [1]
511                          I(L2)/I(L1)     Ratio of Lam2 to Lam1 [1]           
512\                         Type            Histogram type (str) [1]:
513                                           * 'PXC' for constant wavelength x-ray
514                                           * 'PNC' for constant wavelength neutron
515                                           * 'PNT' for time of flight neutron
516\                         Zero            Two-theta zero correction in *degrees* [1]
517\                         Azimuth         Azimuthal setting angle for data recorded
518                                          with differing setting angles [1]
519\                         U, V, W         Cagliotti profile coefficients
520                                          for Gaussian instrumental broadening, where the
521                                          FWHM goes as
522                                          :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
523\                         X, Y            Cauchy (Lorentzian) instrumental broadening
524                                          coefficients [1]
525\                         SH/L            Variant of the Finger-Cox-Jephcoat asymmetric
526                                          peak broadening ratio. Note that this is the
527                                          average between S/L and H/L where S is
528                                          sample height, H is the slit height and
529                                          L is the goniometer diameter. [1]
530\                         Polariz.        Polarization coefficient. [1]
531wtFactor                      \           A weighting factor to increase or decrease
532                                          the leverage of data in the histogram (float).
533                                          A value of 1.0 weights the data with their
534                                          standard uncertainties and a larger value
535                                          increases the weighting of the data (equivalent
536                                          to decreasing the uncertainties).
537Sample Parameters             \           Specifies a dict with parameters that describe how
538                                          the data were collected, as listed
539                                          below. Refinable parameters are a list containing
540                                          a float and a bool, where the second value
541                                          specifies if the value is refined, otherwise
542                                          the value is a float unless otherwise noted.
543\                         Scale           The histogram scale factor (refinable)
544\                         Absorption      The sample absorption coefficient as
545                                          :math:`\\mu r` where r is the radius
546                                          (refinable). Only valid for Debye-Scherrer geometry.
547\                         SurfaceRoughA   Surface roughness parameter A as defined by
548                                          Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable -
549                                          only valid for Bragg-Brentano geometry)                                         
550\                         SurfaceRoughB   Surface roughness parameter B (refinable -
551                                          only valid for Bragg-Brentano geometry)                                         
552\                         DisplaceX,      Sample displacement from goniometer center
553                          DisplaceY       where Y is along the beam direction and
554                                          X is perpendicular. Units are :math:`\\mu m`
555                                          (refinable).
556\                         Phi, Chi,       Goniometer sample setting angles, in degrees.
557                          Omega
558\                         Gonio. radius   Radius of the diffractometer in mm
559\                         InstrName       A name for the instrument, used in preparing
560                                          a CIF (str).
561\                         Force,          Variables that describe how the measurement
562                          Temperature,    was performed. Not used directly in
563                          Humidity,       any computations.
564                          Pressure,
565                          Voltage
566\                         ranId           The random-number Id for the histogram
567                                          (same value as where top-level key is ranId)
568\                         Type            Type of diffraction data, may be 'Debye-Scherrer'
569                                          or 'Bragg-Brentano' (str).
570\                         Diffuse         not in use?
571hId                           \           The number assigned to the histogram when
572                                          the project is loaded or edited (can change)
573ranId                         \           A random number id for the histogram
574                                          that does not change
575Background                    \           The background is stored as a list with where
576                                          the first item in the list is list and the second
577                                          item is a dict. The list contains the background
578                                          function and its coefficients; the dict contains
579                                          Debye diffuse terms and background peaks.
580                                          (TODO: this needs to be expanded.)
581Data                          \           The data consist of a list of 6 np.arrays
582                                          containing in order:
583
584                                           0. the x-postions (two-theta in degrees),
585                                           1. the intensity values (Yobs),
586                                           2. the weights for each Yobs value
587                                           3. the computed intensity values (Ycalc)
588                                           4. the background values
589                                           5. Yobs-Ycalc
590======================  ===============  ====================================================
591
592Powder Reflection Data Structure
593--------------------------------
594
595.. _PowderRefl_table:
596
597.. index::
598   single: Powder reflection object description
599   single: Data object descriptions; Powder Reflections
600   
601For every phase in a histogram, the ``Reflection Lists`` value is a dict
602one element of which is `'RefList'`, which is a np.array containing
603reflections. The columns in that array are documented below.
604
605==========  ====================================================
606  index         explanation
607==========  ====================================================
608 0,1,2       h,k,l (float)
609 3           multiplicity
610 4           d-space, Angstrom
611 5           pos, two-theta
612 6           sig, Gaussian width
613 7           gam, Lorenzian width
614 8           :math:`F_{obs}^2`
615 9           :math:`F_{calc}^2`
616 10          reflection phase, in degrees
617 11          intensity correction for reflection, this times
618             :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
619==========  ====================================================
620
621Single Crystal Tree Items
622-------------------------
623
624.. _Xtal_table:
625
626.. index::
627   single: Single Crystal data object description
628   single: Data object descriptions; Single crystal data
629
630Every single crystal diffraction histogram is stored in the GSAS-II data tree
631with a top-level entry named beginning with the string "HKLF ". The
632diffraction data for that information are directly associated with
633that tree item and there are a series of children to that item. The
634routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
635and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
636load this information into a dictionary where the child tree name is
637used as a key, and the information in the main entry is assigned
638a key of ``Data``, as outlined below.
639
640.. tabularcolumns:: |l|l|p{4in}|
641
642======================  ===============  ====================================================
643  key                      sub-key        explanation
644======================  ===============  ====================================================
645Data                          \           A dict that contains the
646                                          reflection table,
647                                          as described in the
648                                          :ref:`Single Crystal Reflections
649                                          <XtalRefl_table>`
650                                          description.
651
652Instrument Parameters         \           A list containing two dicts where the possible
653                                          keys in each dict are listed below. The value
654                                          for most items is a list containing two values:
655                                          the initial value, the current value.
656                                          The first and second
657                                          values are floats unless otherwise noted.
658\                         Lam             Specifies a wavelength in Angstroms (two floats)
659\                         Type            Histogram type (two str values):
660                                           * 'SXC' for constant wavelength x-ray
661                                           * 'SNC' for constant wavelength neutron
662                                           * 'SNT' for time of flight neutron
663\                         InstrName       A name for the instrument, used in preparing
664                                          a CIF (str).
665
666wtFactor                      \           A weighting factor to increase or decrease
667                                          the leverage of data in the histogram (float).
668                                          A value of 1.0 weights the data with their
669                                          standard uncertainties and a larger value
670                                          increases the weighting of the data (equivalent
671                                          to decreasing the uncertainties).
672
673hId                           \           The number assigned to the histogram when
674                                          the project is loaded or edited (can change)
675ranId                         \           A random number id for the histogram
676                                          that does not change
677======================  ===============  ====================================================
678
679Single Crystal Reflection Data Structure
680----------------------------------------
681
682.. _XtalRefl_table:
683
684.. index::
685   single: Single Crystal reflection object description
686   single: Data object descriptions; Single Crystal Reflections
687   
688For every single crystal a histogram, the ``'Data'`` item contains
689the structure factors as an np.array in item `'RefList'`.
690The columns in that array are documented below.
691
692==========  ====================================================
693  index         explanation
694==========  ====================================================
695 0,1,2       h,k,l (float)
696 3           multiplicity
697 4           d-space, Angstrom
698 5           :math:`F_{obs}^2`
699 6           :math:`\sigma(F_{obs}^2)`
700 7           :math:`F_{calc}^2`
701 8           :math:`F_{obs}^2T`
702 9           :math:`F_{calc}^2T`
703 10          reflection phase, in degrees
704 11          intensity correction for reflection, this times
705             :math:`F_{obs}^2` or :math:`F_{calc}^2`
706             gives Iobs or Icalc
707==========  ====================================================
708
709Image Data Structure
710--------------------
711
712.. _Image_table:
713
714.. index::
715   image: Image data object description
716   image: Image object descriptions
717   
718Every 2-dimensional image is stored in the GSAS-II data tree
719with a top-level entry named beginning with the string "IMG ". The
720image data are directly associated with that tree item and there
721are a series of children to that item. The routines :func:`GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
722and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
723load this information into a dictionary where the child tree name is
724used as a key, and the information in the main entry is assigned
725a key of ``Data``, as outlined below.
726
727.. tabularcolumns:: |l|l|p{4in}|
728
729======================  ======================  ====================================================
730  key                      sub-key              explanation
731======================  ======================  ====================================================
732Comments                       \                Text strings extracted from the original image data
733                                                header or a metafile. These cannot be changed by 
734                                                the user; it may be empty.                                               
735Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
736                                                value. Accomodates
737                                                detector orientations other than with the detector
738                                                X-axis
739                                                horizontal.
740\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
741                                                during image integration multiplied by value. It must have the same size/shape as
742                                                the integrated image. NB: value < 0 for subtraction.
743\                           calibrant           (str) The material used for determining the position/orientation
744                                                of the image. The data is obtained from :func:`ImageCalibrants`
745                                                and UserCalibrants.py (supplied by user).
746\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
747\                           calibskip           (int) The number of expected diffraction lines skipped during the last
748                                                calibration run.
749\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
750                                                strikes the detector plane as determined by calibration. This point
751                                                does not have to be within the limits of the detector boundaries.
752\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
753                                                of the image is at the center line otherwise it is at the leading edge.
754\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
755\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
756                                                calibration calculations. See pixLimit for details as how point is found.           
757\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
758                                                ring offset at higher angles. Optionally determined by calibration.
759\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
760\                           distance            (float) The distance (mm) from sample to detector plane.
761\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
762                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
763                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
764                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
765                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
766\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
767\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
768\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
769                                                Required for texture calculations.
770\                           invert_x            (bool) If True display the image with the x-axis inverted.
771\                           invert_y            (bool) If True display the image with the y-axis inverted.
772\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
773\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
774\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
775                                                intensities obtained during integration.
776\                           outAzimuths         (int) The number of azimuth pie slices.
777\                           outChannels         (int) The number of 2-theta steps.
778\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
779\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
780                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
781                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
782                                                Locations are used to construct rings of points for calibration calcualtions.
783\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
784                                                integration using value.
785\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
786                                                diffraction ring with the same d-spacing (dsp)
787\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
788                                                selected by the user,
789\                           Range               (list) The minimum & maximum values of the image
790\                           rotation            (float) The angle between the x-axis and the vector about which the
791                                                detector is tilted. Constrained to -180 to 180 deg.     
792\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
793                                                calculations.
794\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
795                                                to cause correction to be applied.
796\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
797\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.           
798\                           showLines           (bool) If True then isplay the integration limits to be used.
799\                           size                (list:int) The number of pixels on the image x & y axes
800\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
801\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
802\                           wavelength          (float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).
803                                               
804Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
805                                                to be excluded from integration
806\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
807                                                of which is excluded from recalibration and integration. Only one frame is allowed.
808\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
809                                                from integration.
810\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
811                                                to be excluded from integration.
812\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
813                                                to be excluded from integration.
814\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
815                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.   
816                                               
817Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
818\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
819                                                These will be restricted by space group symmetry; result of strain fit refinement.
820\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
821\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase
822                                                and are used to determine the strain tensor.
823                                                The dictionary items are:
824                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
825                                                'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
826                                                'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
827                                                'Esig': (list: float) Esds for Emat from fitting.
828                                                'pixLimit': (int) Search range to find highest point on ring for each data point
829                                                'cutoff': (float) I/Ib cutoff for searching.
830                                                'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
831                                                'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
832                                                'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
833                                               
834======================  ======================  ====================================================
835
836Parameter Dictionary
837-------------------------
838
839.. _parmDict_table:
840
841.. index::
842   single: Parameter dictionary
843
844The parameter dictionary contains all of the variable parameters for the refinement.
845The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
846It is prepared in two ways. When loaded from the tree
847(in :meth:`GSASIIdataGUI.GSASII.MakeLSParmDict` and
848:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
849the values are lists with two elements: ``[value, refine flag]``
850
851When loaded from the GPX file (in
852:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
853dict is the actual parameter value (usually a float, but sometimes a
854letter or string flag value (such as I or A for iso/anisotropic).
855
856
857*Classes and routines*
858----------------------
859
860'''
861import re
862import imp
863import random as ran
864import sys
865import os.path as ospath
866import cPickle
867import GSASIIpath
868import GSASIImath as G2mth
869import GSASIIspc as G2spc
870import numpy as np
871
872GSASIIpath.SetVersionNumber("$Revision: 2927 $")
873
874DefaultControls = {
875    'deriv type':'analytic Hessian',
876    'min dM/M':0.001,'shift factor':1.,'max cyc':3,'F**2':False,'SVDtol':1.e-6,
877    'UsrReject':{'minF/sig':0,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
878    'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
879    'Author':'no name',
880    'FreePrm1':'Sample humidity (%)',
881    'FreePrm2':'Sample voltage (V)',
882    'FreePrm3':'Applied load (MN)',
883    'ShowCell':False,
884    }
885'''Values to be used as defaults for the initial contents of the ``Controls``
886data tree item.
887'''
888def StripUnicode(string,subs='.'):
889    '''Strip non-ASCII characters from strings
890   
891    :param str string: string to strip Unicode characters from
892    :param str subs: character(s) to place into string in place of each
893      Unicode character. Defaults to '.'
894
895    :returns: a new string with only ASCII characters
896    '''
897    s = ''
898    for c in string:
899        if ord(c) < 128:
900            s += c
901        else:
902            s += subs
903    return s.encode('ascii','replace')
904
905def MakeUniqueLabel(lbl,labellist):
906    '''Make sure that every a label is unique against a list by adding
907    digits at the end until it is not found in list.
908
909    :param str lbl: the input label
910    :param list labellist: the labels that have already been encountered
911    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
912      ``_10-99``, etc.) appended at the end
913    '''
914    lbl = StripUnicode(lbl.strip(),'_')
915    if not lbl: # deal with a blank label
916        lbl = '_1'
917    if lbl not in labellist:
918        labellist.append(lbl)
919        return lbl
920    i = 1
921    prefix = lbl
922    if '_' in lbl:
923        prefix = lbl[:lbl.rfind('_')]
924        suffix = lbl[lbl.rfind('_')+1:]
925        try:
926            i = int(suffix)+1
927        except: # suffix could not be parsed
928            i = 1
929            prefix = lbl
930    while prefix+'_'+str(i) in labellist:
931        i += 1
932    else:
933        lbl = prefix+'_'+str(i)
934        labellist.append(lbl)
935    return lbl
936
937PhaseIdLookup = {}
938'''dict listing phase name and random Id keyed by sequential phase index as a str;
939best to access this using :func:`LookupPhaseName`
940'''
941PhaseRanIdLookup = {}
942'''dict listing phase sequential index keyed by phase random Id;
943best to access this using :func:`LookupPhaseId`
944'''
945HistIdLookup = {}
946'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
947best to access this using :func:`LookupHistName`
948'''
949HistRanIdLookup = {}
950'''dict listing histogram sequential index keyed by histogram random Id;
951best to access this using :func:`LookupHistId`
952'''
953AtomIdLookup = {}
954'''dict listing for each phase index as a str, the atom label and atom random Id,
955keyed by atom sequential index as a str;
956best to access this using :func:`LookupAtomLabel`
957'''
958AtomRanIdLookup = {}
959'''dict listing for each phase the atom sequential index keyed by atom random Id;
960best to access this using :func:`LookupAtomId`
961'''
962ShortPhaseNames = {}
963'''a dict containing a possibly shortened and when non-unique numbered
964version of the phase name. Keyed by the phase sequential index.
965'''
966ShortHistNames = {}
967'''a dict containing a possibly shortened and when non-unique numbered
968version of the histogram name. Keyed by the histogram sequential index.
969'''
970
971VarDesc = {}
972''' This dictionary lists descriptions for GSAS-II variables,
973as set in :func:`CompileVarDesc`. See that function for a description
974for how keys and values are written.
975'''
976
977reVarDesc = {}
978''' This dictionary lists descriptions for GSAS-II variables with
979the same values as :attr:`VarDesc` except that keys have been compiled as
980regular expressions. Initialized in :func:`CompileVarDesc`.
981'''
982# create a default space group object for P1; N.B. fails when building documentation
983try: 
984    P1SGData = G2spc.SpcGroup('P 1')[1] # data structure for default space group
985except TypeError:
986    pass
987
988def GetPhaseNames(fl):
989    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
990    NB: there is another one of these in GSASIIstrIO.py that uses the gpx filename
991
992    :param file fl: opened .gpx file
993    :return: list of phase names
994    '''
995    PhaseNames = []
996    while True:
997        try:
998            data = cPickle.load(fl)
999        except EOFError:
1000            break
1001        datum = data[0]
1002        if 'Phases' == datum[0]:
1003            for datus in data[1:]:
1004                PhaseNames.append(datus[0])
1005    fl.seek(0)          #reposition file
1006    return PhaseNames
1007
1008def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1009    '''Create a new phase dict with default values for various parameters
1010
1011    :param str Name: Name for new Phase
1012
1013    :param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1014      defaults to data for P 1
1015
1016    :param list cell: unit cell parameter list; defaults to
1017      [1.0,1.0,1.0,90.,90,90.,1.]
1018
1019    '''
1020    if SGData is None: SGData = P1SGData
1021    if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1022    phaseData = {
1023        'ranId':ran.randint(0,sys.maxint),
1024        'General':{
1025            'Name':Name,
1026            'Type':'nuclear',
1027            'Modulated':False,
1028            'AtomPtrs':[3,1,7,9],
1029            'SGData':SGData,
1030            'Cell':[False,]+cell,
1031            'Pawley dmin':1.0,
1032            'Data plot type':'None',
1033            'SH Texture':{
1034                'Order':0,
1035                'Model':'cylindrical',
1036                'Sample omega':[False,0.0],
1037                'Sample chi':[False,0.0],
1038                'Sample phi':[False,0.0],
1039                'SH Coeff':[False,{}],
1040                'SHShow':False,
1041                'PFhkl':[0,0,1],
1042                'PFxyz':[0,0,1],
1043                'PlotType':'Pole figure',
1044                'Penalty':[['',],0.1,False,1.0]}},
1045        'Atoms':[],
1046        'Drawing':{},
1047        'Histograms':{},
1048        'Pawley ref':[],
1049        'RBModels':{},
1050        }
1051    if Super and Super.get('Use',False):
1052        phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1053        phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1054        phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1055
1056    return phaseData
1057               
1058def ReadCIF(URLorFile):
1059    '''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
1060    (from James Hester).
1061    The open routine gets confused with DOS names that begin with a letter and colon
1062    "C:\dir\" so this routine will try to open the passed name as a file and if that
1063    fails, try it as a URL
1064
1065    :param str URLorFile: string containing a URL or a file name. Code will try first
1066      to open it as a file and then as a URL.
1067
1068    :returns: a PyCifRW CIF object.
1069    '''
1070    import CifFile as cif # PyCifRW from James Hester
1071
1072    # alternate approach:
1073    #import urllib
1074    #ciffile = 'file:'+urllib.pathname2url(filename)
1075   
1076    try:
1077        fp = open(URLorFile,'r')
1078        cf = cif.ReadCif(fp)
1079        fp.close()
1080        return cf
1081    except IOError:
1082        return cif.ReadCif(URLorFile)
1083
1084def IndexAllIds(Histograms,Phases):
1085    '''Scan through the used phases & histograms and create an index
1086    to the random numbers of phases, histograms and atoms. While doing this,
1087    confirm that assigned random numbers are unique -- just in case lightning
1088    strikes twice in the same place.
1089
1090    Note: this code assumes that the atom random Id (ranId) is the last
1091    element each atom record.
1092
1093    This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
1094    (which loads the histograms and phases from a GPX file),
1095    :meth:`~GSASIIdataGUI.GSASII.GetUsedHistogramsAndPhasesfromTree`
1096    (which loads the histograms and phases from the data tree.) and
1097    :meth:`GSASIIconstrGUI.UpdateConstraints`
1098    (which displays & edits the constraints in a GUI)
1099
1100    TODO: do we need a lookup for rigid body variables?
1101    '''
1102    # process phases and atoms
1103    PhaseIdLookup.clear()
1104    PhaseRanIdLookup.clear()   
1105    AtomIdLookup.clear()
1106    AtomRanIdLookup.clear()
1107    ShortPhaseNames.clear()
1108    for ph in Phases:
1109        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
1110        ranId = Phases[ph]['ranId'] 
1111        while ranId in PhaseRanIdLookup:
1112            # Found duplicate random Id! note and reassign
1113            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
1114            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxint)
1115        pId = str(Phases[ph]['pId'])
1116        PhaseIdLookup[pId] = (ph,ranId)
1117        PhaseRanIdLookup[ranId] = pId
1118        shortname = ph  #[:10]
1119        while shortname in ShortPhaseNames.values():
1120            shortname = ph[:8] + ' ('+ pId + ')'
1121        ShortPhaseNames[pId] = shortname
1122        AtomIdLookup[pId] = {}
1123        AtomRanIdLookup[pId] = {}
1124        for iatm,at in enumerate(Phases[ph]['Atoms']):
1125            ranId = at[cia+8]
1126            while ranId in AtomRanIdLookup[pId]: # check for dups
1127                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
1128                at[cia+8] = ranId = ran.randint(0,sys.maxint)
1129            AtomRanIdLookup[pId][ranId] = str(iatm)
1130            if Phases[ph]['General']['Type'] == 'macromolecular':
1131                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1132            else:
1133                label = at[ct-1]
1134            AtomIdLookup[pId][str(iatm)] = (label,ranId)
1135    # process histograms
1136    HistIdLookup.clear()
1137    HistRanIdLookup.clear()
1138    ShortHistNames.clear()
1139    for hist in Histograms:
1140        ranId = Histograms[hist]['ranId']
1141        while ranId in HistRanIdLookup:
1142            # Found duplicate random Id! note and reassign
1143            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
1144            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxint)
1145        hId = str(Histograms[hist]['hId'])
1146        HistIdLookup[hId] = (hist,ranId)
1147        HistRanIdLookup[ranId] = hId
1148        shortname = hist[:15]
1149        while shortname in ShortHistNames.values():
1150            shortname = hist[:11] + ' ('+ hId + ')'
1151        ShortHistNames[hId] = shortname
1152
1153def LookupAtomId(pId,ranId):
1154    '''Get the atom number from a phase and atom random Id
1155
1156    :param int/str pId: the sequential number of the phase
1157    :param int ranId: the random Id assigned to an atom
1158
1159    :returns: the index number of the atom (str)
1160    '''
1161    if not AtomRanIdLookup:
1162        raise Exception,'Error: LookupAtomId called before IndexAllIds was run'
1163    if pId is None or pId == '':
1164        raise KeyError,'Error: phase is invalid (None or blank)'
1165    pId = str(pId)
1166    if pId not in AtomRanIdLookup:
1167        raise KeyError,'Error: LookupAtomId does not have phase '+pId
1168    if ranId not in AtomRanIdLookup[pId]:
1169        raise KeyError,'Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']'
1170    return AtomRanIdLookup[pId][ranId]
1171
1172def LookupAtomLabel(pId,index):
1173    '''Get the atom label from a phase and atom index number
1174
1175    :param int/str pId: the sequential number of the phase
1176    :param int index: the index of the atom in the list of atoms
1177
1178    :returns: the label for the atom (str) and the random Id of the atom (int)
1179    '''
1180    if not AtomIdLookup:
1181        raise Exception,'Error: LookupAtomLabel called before IndexAllIds was run'
1182    if pId is None or pId == '':
1183        raise KeyError,'Error: phase is invalid (None or blank)'
1184    pId = str(pId)
1185    if pId not in AtomIdLookup:
1186        raise KeyError,'Error: LookupAtomLabel does not have phase '+pId
1187    if index not in AtomIdLookup[pId]:
1188        raise KeyError,'Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']'
1189    return AtomIdLookup[pId][index]
1190
1191def LookupPhaseId(ranId):
1192    '''Get the phase number and name from a phase random Id
1193
1194    :param int ranId: the random Id assigned to a phase
1195    :returns: the sequential Id (pId) number for the phase (str)
1196    '''
1197    if not PhaseRanIdLookup:
1198        raise Exception,'Error: LookupPhaseId called before IndexAllIds was run'
1199    if ranId not in PhaseRanIdLookup:
1200        raise KeyError,'Error: LookupPhaseId does not have ranId '+str(ranId)
1201    return PhaseRanIdLookup[ranId]
1202
1203def LookupPhaseName(pId):
1204    '''Get the phase number and name from a phase Id
1205
1206    :param int/str pId: the sequential assigned to a phase
1207    :returns:  (phase,ranId) where phase is the name of the phase (str)
1208      and ranId is the random # id for the phase (int)
1209    '''
1210    if not PhaseIdLookup:
1211        raise Exception,'Error: LookupPhaseName called before IndexAllIds was run'
1212    if pId is None or pId == '':
1213        raise KeyError,'Error: phase is invalid (None or blank)'
1214    pId = str(pId)
1215    if pId not in PhaseIdLookup:
1216        raise KeyError,'Error: LookupPhaseName does not have index '+pId
1217    return PhaseIdLookup[pId]
1218
1219def LookupHistId(ranId):
1220    '''Get the histogram number and name from a histogram random Id
1221
1222    :param int ranId: the random Id assigned to a histogram
1223    :returns: the sequential Id (hId) number for the histogram (str)
1224    '''
1225    if not HistRanIdLookup:
1226        raise Exception,'Error: LookupHistId called before IndexAllIds was run'
1227    if ranId not in HistRanIdLookup:
1228        raise KeyError,'Error: LookupHistId does not have ranId '+str(ranId)
1229    return HistRanIdLookup[ranId]
1230
1231def LookupHistName(hId):
1232    '''Get the histogram number and name from a histogram Id
1233
1234    :param int/str hId: the sequential assigned to a histogram
1235    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1236      and ranId is the random # id for the histogram (int)
1237    '''
1238    if not HistIdLookup:
1239        raise Exception,'Error: LookupHistName called before IndexAllIds was run'
1240    if hId is None or hId == '':
1241        raise KeyError,'Error: histogram is invalid (None or blank)'
1242    hId = str(hId)
1243    if hId not in HistIdLookup:
1244        raise KeyError,'Error: LookupHistName does not have index '+hId
1245    return HistIdLookup[hId]
1246
1247def fmtVarDescr(varname):
1248    '''Return a string with a more complete description for a GSAS-II variable
1249
1250    :param str varname: A full G2 variable name with 2 or 3 or 4
1251       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1252       
1253    :returns: a string with the description
1254    '''
1255    s,l = VarDescr(varname)
1256    return s+": "+l
1257
1258def VarDescr(varname):
1259    '''Return two strings with a more complete description for a GSAS-II variable
1260
1261    :param str name: A full G2 variable name with 2 or 3 or 4
1262       colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
1263       
1264    :returns: (loc,meaning) where loc describes what item the variable is mapped
1265      (phase, histogram, etc.) and meaning describes what the variable does.
1266    '''
1267   
1268    # special handling for parameter names without a colons
1269    # for now, assume self-defining
1270    if varname.find(':') == -1:
1271        return "Global",varname
1272       
1273    l = getVarDescr(varname)
1274    if not l:
1275        return ("invalid variable name ("+str(varname)+")!"),""
1276#        return "invalid variable name!",""
1277
1278    if not l[-1]:
1279        l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
1280
1281    if len(l) == 3:         #SASD variable name!
1282        s = 'component:'+l[1]
1283        return s,l[-1]
1284    s = ""
1285    if l[0] is not None and l[1] is not None: # HAP: keep short
1286        if l[2] == "Scale": # fix up ambigous name
1287            l[5] = "Phase fraction"
1288        if l[0] == '*':
1289            lbl = 'Seq. ref.'
1290        else:
1291            lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1292        if l[1] == '*':
1293            hlbl = 'Seq. ref.'
1294        else:
1295            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1296        if hlbl[:4] == 'HKLF':
1297            hlbl = 'Xtl='+hlbl[5:]
1298        elif hlbl[:4] == 'PWDR':
1299            hlbl = 'Pwd='+hlbl[5:]
1300        else:
1301            hlbl = 'Hist='+hlbl
1302        s = "Ph="+str(lbl)+" * "+str(hlbl)
1303    else:
1304        if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
1305            l[5] = "Scale factor"
1306        if l[2] == 'Back': # background parameters are "special", alas
1307            s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
1308            l[-1] += ' #'+str(l[3])
1309        elif l[4] is not None: # rigid body parameter or modulation parm
1310            lbl = ShortPhaseNames.get(l[0],'phase?')
1311            if 'RB' in l[2]:    #rigid body parm
1312                s = "Res #"+str(l[3])+" body #"+str(l[4])+" in "+str(lbl)
1313            else: #modulation parm
1314                s = 'Atom %s wave %s in %s'%(LookupAtomLabel(l[0],l[3])[0],l[4],lbl)
1315        elif l[3] is not None: # atom parameter,
1316            lbl = ShortPhaseNames.get(l[0],'phase?')
1317            try:
1318                albl = LookupAtomLabel(l[0],l[3])[0]
1319            except KeyError:
1320                albl = 'Atom?'
1321            s = "Atom "+str(albl)+" in "+str(lbl)
1322        elif l[0] == '*':
1323            s = "All phases "
1324        elif l[0] is not None:
1325            lbl = ShortPhaseNames.get(l[0],'phase?')
1326            s = "Phase "+str(lbl)
1327        elif l[1] == '*':
1328            s = 'All hists'
1329        elif l[1] is not None:
1330            hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1331            if hlbl[:4] == 'HKLF':
1332                hlbl = 'Xtl='+hlbl[5:]
1333            elif hlbl[:4] == 'PWDR':
1334                hlbl = 'Pwd='+hlbl[5:]
1335            else:
1336                hlbl = 'Hist='+hlbl
1337            s = str(hlbl)
1338    if not s:
1339        s = 'Global'
1340    return s,l[-1]
1341
1342def getVarDescr(varname):
1343    '''Return a short description for a GSAS-II variable
1344
1345    :param str name: A full G2 variable name with 2 or 3 or 4
1346       colons (<p>:<h>:name[:<a1>][:<a2>])
1347     
1348    :returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
1349      where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
1350      the histogram number and the atom number; `name` will always be
1351      a str; and `description` is str or `None`.
1352      If the variable name is incorrectly formed (for example, wrong
1353      number of colons), `None` is returned instead of a list.
1354    '''
1355    l = varname.split(':')
1356    if len(l) == 2:     #SASD parameter name
1357        return varname,l[0],getDescr(l[1])
1358    if len(l) == 3:
1359        l += [None,None]
1360    elif len(l) == 4:
1361        l += [None]
1362    elif len(l) != 5:
1363        return None
1364    for i in (0,1,3,4):
1365        if l[i] == "":
1366            l[i] = None
1367    l += [getDescr(l[2])]
1368    return l
1369   
1370def CompileVarDesc():
1371    '''Set the values in the variable description lookup table (:attr:`VarDesc`)
1372    into :attr:`reVarDesc`. This is called in :func:`getDescr` so the initialization
1373    is always done before use.
1374
1375    Note that keys may contain regular expressions, where '[xyz]'
1376    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range of values).
1377    '.*' matches any string. For example::
1378
1379    'AUiso':'Atomic isotropic displacement parameter',
1380
1381    will match variable ``'p::AUiso:a'``.
1382    If parentheses are used in the key, the contents of those parentheses can be
1383    used in the value, such as::
1384
1385    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1386
1387    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1388    in the value when used.
1389   
1390    '''
1391    if reVarDesc: return # already done
1392    for key,value in {
1393        # derived or other sequential vars
1394        '([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
1395        u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
1396        u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
1397        u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
1398        # ambiguous, alas:
1399        'Scale' : 'Phase or Histogram scale factor',
1400        # Phase vars (p::<var>)
1401        'A([0-5])' : 'Reciprocal metric tensor component \\1',
1402        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
1403        # Atom vars (p::<var>:a)
1404        'dA([xyz])$' : 'change to atomic coordinate, \\1',
1405        'A([xyz])$' : '\\1 fractional atomic coordinate',
1406        'AUiso':'Atomic isotropic displacement parameter',
1407        'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1408        'Afrac': 'Atomic site fraction parameter',
1409        'Amul': 'Atomic site multiplicity value',
1410        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
1411        # Hist & Phase (HAP) vars (p:h:<var>)
1412        'Back': 'Background term',
1413        'BkPkint;(.*)':'Background peak #\\1 intensity',
1414        'BkPkpos;(.*)':'Background peak #\\1 position',
1415        'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
1416        'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
1417        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1418        'D([123][123])' : 'Anisotropic strain coef. \\1',
1419        'Extinction' : 'Extinction coef.',
1420        'MD' : 'March-Dollase coef.',
1421        'Mustrain;.*' : 'Microstrain coef.',
1422        'Size;.*' : 'Crystallite size value',
1423        'eA$' : 'Cubic mustrain value',
1424        'Ep$' : 'Primary extinction',
1425        'Es$' : 'Secondary type II extinction',
1426        'Eg$' : 'Secondary type I extinction',
1427        'Flack' : 'Flack parameter',
1428        'TwinFr' : 'Twin fraction',
1429        #Histogram vars (:h:<var>)
1430        'Absorption' : 'Absorption coef.',
1431        'Displace([XY])' : 'Debye-Scherrer sample displacement \\1',
1432        'Lam' : 'Wavelength',
1433        'Polariz\.' : 'Polarization correction',
1434        'SH/L' : 'FCJ peak asymmetry correction',
1435        '([UVW])$' : 'Gaussian instrument broadening \\1',
1436        '([XY])$' : 'Cauchy instrument broadening \\1',
1437        'Zero' : 'Debye-Scherrer zero correction',
1438        'nDebye' : 'Debye model background corr. terms',
1439        'nPeaks' : 'Fixed peak background corr. terms',
1440        'RBV.*' : 'Vector rigid body parameter',
1441        'RBR.*' : 'Residue rigid body parameter',
1442        'RBRO([aijk])' : 'Residue rigid body orientation parameter',
1443        'RBRP([xyz])' : 'Residue rigid body position parameter',
1444        'RBRTr;.*' : 'Residue rigid body torsion parameter',
1445        'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
1446        'constr([0-9]*)' : 'Parameter from constraint',
1447        # supersymmetry parameters  p::<var>:a:o 'Flen','Fcent'?
1448        'mV([0-2])$' : 'Modulation vector component \\1',
1449        'Fsin'  :   'Sin site fraction modulation',
1450        'Fcos'  :   'Cos site fraction modulation',
1451        'Fzero'  :   'Crenel function offset',      #may go away
1452        'Fwid'   :   'Crenel function width',
1453        'Tmin'   :   'ZigZag/Block min location',
1454        'Tmax'   :   'ZigZag/Block max location',
1455        '([XYZ])max': 'ZigZag/Block max value for \\1',
1456        '([XYZ])sin'  : 'Sin position wave for \\1',
1457        '([XYZ])cos'  : 'Cos position wave for \\1',
1458        'U([123][123])sin$' :  'Sin thermal wave for U\\1',
1459        'U([123][123])cos$' :  'Cos thermal wave for U\\1',
1460        'M([XYZ])sin$' :  'Sin mag. moment wave for \\1',
1461        'M([XYZ])cos$' :  'Cos mag. moment wave for \\1',
1462        # PDF peak parms (l:<var>;l = peak no.)
1463        'PDFpos'  : 'PDF peak position',
1464        'PDFmag'  : 'PDF peak magnitude',
1465        'PDFsig'  : 'PDF peak std. dev.',
1466        # SASD vars (l:<var>;l = component)
1467        'Aspect ratio' : 'Particle aspect ratio',
1468        'Length' : 'Cylinder length',
1469        'Diameter' : 'Cylinder/disk diameter',
1470        'Thickness' : 'Disk thickness',
1471        'Shell thickness' : 'Multiplier to get inner(<1) or outer(>1) sphere radius',
1472        'Dist' : 'Interparticle distance',
1473        'VolFr' : 'Dense scatterer volume fraction',
1474        'epis' : 'Sticky sphere epsilon',
1475        'Sticky' : 'Stickyness',
1476        'Depth' : 'Well depth',
1477        'Width' : 'Well width',
1478        'Volume' : 'Particle volume',
1479        'Radius' : 'Sphere/cylinder/disk radius',
1480        'Mean' : 'Particle mean radius',
1481        'StdDev' : 'Standard deviation in Mean',
1482        'G$': 'Guinier prefactor',
1483        'Rg$': 'Guinier radius of gyration',
1484        'B$': 'Porod prefactor',
1485        'P$': 'Porod power',
1486        'Cutoff': 'Porod cutoff',
1487        'PkInt': 'Bragg peak intensity',
1488        'PkPos': 'Bragg peak position',
1489        'PkSig': 'Bragg peak sigma',
1490        'PkGam': 'Bragg peak gamma',
1491        'e([12][12])' : 'strain tensor e\1',   # strain vars e11, e22, e12
1492        'Dcalc': 'Calc. d-spacing',
1493        'Back$': 'background parameter',
1494        'pos$': 'peak position',
1495        'int$': 'peak intensity',
1496        'WgtFrac':'phase weight fraction',
1497        }.items():
1498        VarDesc[key] = value
1499        reVarDesc[re.compile(key)] = value
1500
1501def getDescr(name):
1502    '''Return a short description for a GSAS-II variable
1503
1504    :param str name: The descriptive part of the variable name without colons (:)
1505     
1506    :returns: a short description or None if not found
1507    '''
1508
1509    CompileVarDesc() # compile the regular expressions, if needed
1510    for key in reVarDesc:
1511        m = key.match(name)
1512        if m:
1513            reVarDesc[key]
1514            return m.expand(reVarDesc[key])
1515    return None
1516
1517def GenWildCard(varlist):
1518    '''Generate wildcard versions of G2 variables. These introduce '*'
1519    for a phase, histogram or atom number (but only for one of these
1520    fields) but only when there is more than one matching variable in the
1521    input variable list. So if the input is this::
1522   
1523      varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
1524
1525    then the output will be this::
1526   
1527       wildList = ['*::AUiso:0', '0::AUiso:*']
1528
1529    :param list varlist: an input list of GSAS-II variable names
1530      (such as 0::AUiso:0)
1531
1532    :returns: wildList, the generated list of wild card variable names.
1533    '''
1534    wild = []
1535    for i in (0,1,3):
1536        currentL = varlist[:]
1537        while currentL:
1538            item1 = currentL.pop(0)
1539            i1splt = item1.split(':')
1540            if i >= len(i1splt): continue
1541            if i1splt[i]:
1542                nextL = []
1543                i1splt[i] = '[0-9]+'
1544                rexp = re.compile(':'.join(i1splt))
1545                matchlist = [item1]
1546                for nxtitem in currentL:
1547                    if rexp.match(nxtitem):
1548                        matchlist += [nxtitem]
1549                    else:
1550                        nextL.append(nxtitem)
1551                if len(matchlist) > 1:
1552                    i1splt[i] = '*'
1553                    wild.append(':'.join(i1splt))
1554                currentL = nextL
1555    return wild
1556
1557def LookupWildCard(varname,varlist):
1558    '''returns a list of variable names from list varname
1559    that match wildcard name in varname
1560   
1561    :param str varname: a G2 variable name containing a wildcard
1562      (such as \*::var)
1563    :param list varlist: the list of all variable names used in
1564      the current project
1565    :returns: a list of matching GSAS-II variables (may be empty) 
1566    '''
1567    rexp = re.compile(varname.replace('*','[0-9]+'))
1568    return sorted([var for var in varlist if rexp.match(var)])
1569
1570
1571def _lookup(dic,key):
1572    '''Lookup a key in a dictionary, where None returns an empty string
1573    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
1574    '''
1575    if key is None:
1576        return ""
1577    elif key == "*":
1578        return "*"
1579    else:
1580        return dic.get(key,'?')
1581
1582class G2VarObj(object):
1583    '''Defines a GSAS-II variable either using the phase/atom/histogram
1584    unique Id numbers or using a character string that specifies
1585    variables by phase/atom/histogram number (which can change).
1586    Note that :func:`LoadID` should be used to (re)load the current Ids
1587    before creating or later using the G2VarObj object.
1588
1589    This can store rigid body variables, but does not translate the residue # and
1590    body # to/from random Ids
1591
1592    A :class:`G2VarObj` object can be created with a single parameter:
1593   
1594    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
1595      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
1596
1597     * p is the phase number (which may be left blank or may be '*' to indicate all phases);
1598     * h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
1599     * a is the atom number (which may be left blank in which case the third colon is omitted).
1600       The atom number can be specified as '*' if a phase number is specified (not as '*').
1601       For rigid body variables, specify a will be a string of form "residue:body#"
1602
1603      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
1604      Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
1605      and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
1606      For a rigid body variables, AtomID is a string of form "residue:body#".
1607
1608    If four positional arguments are supplied, they are:
1609
1610    :param str/int phasenum: The number for the phase (or None or '*')
1611    :param str/int histnum: The number for the histogram (or None or '*')
1612    :param str varname: a single value can be used to create a :class:`G2VarObj`
1613    :param str/int atomnum: The number for the atom (or None or '*')
1614   
1615    '''
1616    IDdict = {}
1617    IDdict['phases'] = {}
1618    IDdict['hists'] = {}
1619    IDdict['atoms'] = {}
1620    def __init__(self,*args):
1621        self.phase = None
1622        self.histogram = None
1623        self.name = ''
1624        self.atom = None
1625        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
1626            # single arg with 4 values
1627            self.phase,self.histogram,self.name,self.atom = args[0]
1628        elif len(args) == 1 and ':' in args[0]:
1629            #parse a string
1630            lst = args[0].split(':')
1631            if lst[0] == '*':
1632                self.phase = '*'
1633                if len(lst) > 3:
1634                    self.atom = lst[3]
1635                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1636            elif lst[1] == '*':           
1637                self.histogram = '*'
1638                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1639            else:
1640                self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1641                self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1642                if len(lst) == 4:
1643                    if lst[3] == '*':
1644                        self.atom = '*'
1645                    else:
1646                        self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
1647                elif len(lst) == 5:
1648                    self.atom = lst[3]+":"+lst[4]
1649                elif len(lst) == 3:
1650                    pass
1651                else:
1652                    raise Exception,"Too many colons in var name "+str(args[0])
1653            self.name = lst[2]
1654        elif len(args) == 4:
1655            if args[0] == '*':
1656                self.phase = '*'
1657                self.atom = args[3]
1658            else:
1659                self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
1660                if args[3] == '*':
1661                    self.atom = '*'
1662                elif args[0] is not None:
1663                    self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
1664            if args[1] == '*':
1665                self.histogram = '*'
1666            else:
1667                self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
1668            self.name = args[2]
1669        else:
1670            raise Exception,"Incorrectly called GSAS-II parameter name"
1671
1672        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
1673
1674    def __str__(self):
1675        return self.varname()
1676
1677    def varname(self):
1678        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
1679        string (p:h:<var>:a) or (p:h:<var>)
1680
1681        :returns: the variable name as a str
1682        '''
1683        a = ""
1684        if self.phase == "*":
1685            ph = "*"
1686            if self.atom:
1687                a = ":" + str(self.atom)
1688        else:
1689            ph = _lookup(PhaseRanIdLookup,self.phase)
1690            if self.atom == '*':
1691                a = ':*'
1692            elif self.atom:
1693                if ":" in str(self.atom):
1694                    a = ":" + str(self.atom)
1695                elif ph in AtomRanIdLookup:
1696                    a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
1697                else:
1698                    a = ":?"
1699        if self.histogram == "*":
1700            hist = "*"
1701        else:
1702            hist = _lookup(HistRanIdLookup,self.histogram)
1703        s = (ph + ":" + hist + ":" + str(self.name)) + a
1704        return s
1705   
1706    def __repr__(self):
1707        '''Return the detailed contents of the object
1708        '''
1709        s = "<"
1710        if self.phase == '*':
1711            s += "Phases: all; "
1712            if self.atom is not None:
1713                if ":" in str(self.atom):
1714                    s += "Rigid body" + str(self.atom) + "; "
1715                else:
1716                    s += "Atom #" + str(self.atom) + "; "
1717        elif self.phase is not None:
1718            ph =  _lookup(PhaseRanIdLookup,self.phase)
1719            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
1720            if self.atom == '*':
1721                s += "Atoms: all; "
1722            elif ":" in str(self.atom):
1723                s += "Rigid body" + str(self.atom) + "; "
1724            elif self.atom is not None:
1725                s += "Atom rId=" + str(self.atom)
1726                if ph in AtomRanIdLookup:
1727                    s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
1728                else:
1729                    s += " (#? -- not found!); "
1730        if self.histogram == '*':
1731            s += "Histograms: all; "
1732        elif self.histogram is not None:
1733            hist = _lookup(HistRanIdLookup,self.histogram)
1734            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
1735        s += 'Variable name="' + str(self.name) + '">'
1736        return s+" ("+self.varname()+")"
1737
1738    def __eq__(self, other):
1739        if type(other) is type(self):
1740            return (self.phase == other.phase and
1741                    self.histogram == other.histogram and
1742                    self.name == other.name and
1743                    self.atom == other.atom)
1744        return False
1745
1746    def _show(self):
1747        'For testing, shows the current lookup table'
1748        print 'phases', self.IDdict['phases']
1749        print 'hists', self.IDdict['hists']
1750        print 'atomDict', self.IDdict['atoms']
1751
1752#==========================================================================
1753def SetDefaultSample():
1754    'Fills in default items for the Sample dictionary for Debye-Scherrer & SASD'
1755    return {
1756        'InstrName':'',
1757        'ranId':ran.randint(0,sys.maxint),
1758        'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],
1759        'DisplaceX':[0.0,False],'DisplaceY':[0.0,False],'Diffuse':[],
1760        'Temperature':300.,'Pressure':0.1,'Time':0.0,
1761        'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
1762        'Gonio. radius':200.0,
1763        'Omega':0.0,'Chi':0.0,'Phi':0.0,'Azimuth':0.0,
1764#SASD items
1765        'Materials':[{'Name':'vacuum','VolFrac':1.0,},{'Name':'vacuum','VolFrac':0.0,}],
1766        'Thick':1.0,'Contrast':[0.0,0.0],       #contrast & anomalous contrast
1767        'Trans':1.0,                            #measured transmission
1768        'SlitLen':0.0,                          #Slit length - in Q(A-1)
1769        }
1770######################################################################
1771class ImportBaseclass(object):
1772    '''Defines a base class for the reading of input files (diffraction
1773    data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1774    for an explanation on how to use a subclass of this class.
1775    '''
1776    class ImportException(Exception):
1777        '''Defines an Exception that is used when an import routine hits an expected error,
1778        usually in .Reader.
1779
1780        Good practice is that the Reader should define a value in self.errors that
1781        tells the user some information about what is wrong with their file.         
1782        '''
1783        pass
1784   
1785    UseReader = True  # in __init__ set value of self.UseReader to False to skip use of current importer
1786    def __init__(self,formatName,longFormatName=None,
1787                 extensionlist=[],strictExtension=False,):
1788        self.formatName = formatName # short string naming file type
1789        if longFormatName: # longer string naming file type
1790            self.longFormatName = longFormatName
1791        else:
1792            self.longFormatName = formatName
1793        # define extensions that are allowed for the file type
1794        # for windows, remove any extensions that are duplicate, as case is ignored
1795        if sys.platform == 'windows' and extensionlist:
1796            extensionlist = list(set([s.lower() for s in extensionlist]))
1797        self.extensionlist = extensionlist
1798        # If strictExtension is True, the file will not be read, unless
1799        # the extension matches one in the extensionlist
1800        self.strictExtension = strictExtension
1801        self.errors = ''
1802        self.warnings = ''
1803        self.SciPy = False          #image reader needed scipy
1804        # used for readers that will use multiple passes to read
1805        # more than one data block
1806        self.repeat = False
1807        self.selections = []
1808        self.repeatcount = 0
1809        self.readfilename = '?'
1810        self.scriptable = False
1811        #print 'created',self.__class__
1812
1813    def ReInitialize(self):
1814        'Reinitialize the Reader to initial settings'
1815        self.errors = ''
1816        self.warnings = ''
1817        self.SciPy = False          #image reader needed scipy
1818        self.repeat = False
1819        self.repeatcount = 0
1820        self.readfilename = '?'
1821
1822       
1823#    def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1824#        '''This method must be supplied in the child class to read the file.
1825#        if the read fails either return False or raise an Exception
1826#        preferably of type ImportException.
1827#        '''
1828#        #start reading
1829#        raise ImportException("Error occurred while...")
1830#        self.errors += "Hint for user on why the error occur
1831#        return False # if an error occurs
1832#        return True # if read OK
1833
1834    def ExtensionValidator(self, filename):
1835        '''This methods checks if the file has the correct extension
1836        Return False if this filename will not be supported by this reader
1837        Return True if the extension matches the list supplied by the reader
1838        Return None if the reader allows un-registered extensions
1839        '''
1840        if filename:
1841            ext = ospath.splitext(filename)[1]
1842            if sys.platform == 'windows': ext = ext.lower()
1843            if ext in self.extensionlist: return True
1844            if self.strictExtension: return False
1845        return None
1846
1847    def ContentsValidator(self, filepointer):
1848        '''This routine will attempt to determine if the file can be read
1849        with the current format.
1850        This will typically be overridden with a method that
1851        takes a quick scan of [some of]
1852        the file contents to do a "sanity" check if the file
1853        appears to match the selected format.
1854        '''
1855        #filepointer.seek(0) # rewind the file pointer
1856        return True
1857
1858    def CIFValidator(self, filepointer):
1859        '''A :meth:`ContentsValidator` for use to validate CIF files.
1860        '''
1861        for i,l in enumerate(filepointer):
1862            if i >= 1000: return True
1863            '''Encountered only blank lines or comments in first 1000
1864            lines. This is unlikely, but assume it is CIF anyway, since we are
1865            even less likely to find a file with nothing but hashes and
1866            blank lines'''
1867            line = l.strip()
1868            if len(line) == 0: # ignore blank lines
1869                continue 
1870            elif line.startswith('#'): # ignore comments
1871                continue 
1872            elif line.startswith('data_'): # on the right track, accept this file
1873                return True
1874            else: # found something invalid
1875                self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1876                if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1877                    self.errors += '  '+str(l)
1878                else: 
1879                    self.errors += '  (binary)'
1880                self.errors += '\n  Note: a CIF should only have blank lines or comments before'
1881                self.errors += '\n        a data_ statement begins a block.'
1882                return False 
1883
1884######################################################################
1885class ImportPhase(ImportBaseclass):
1886    '''Defines a base class for the reading of files with coordinates
1887
1888    Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1889    in :meth:`GSASIIdataGUI.GSASII.OnImportPhase`.
1890    See :ref:`Writing a Import Routine<Import_Routines>`
1891    for an explanation on how to use this class.
1892
1893    '''
1894    def __init__(self,formatName,longFormatName=None,extensionlist=[],
1895        strictExtension=False,):
1896        # call parent __init__
1897        ImportBaseclass.__init__(self,formatName,longFormatName,
1898            extensionlist,strictExtension)
1899        self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1900        self.Constraints = None
1901
1902######################################################################
1903class ImportStructFactor(ImportBaseclass):
1904    '''Defines a base class for the reading of files with tables
1905    of structure factors.
1906
1907    Structure factors are read with a call to :meth:`GSASIIdataGUI.GSASII.OnImportSfact`
1908    which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`, which calls
1909    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1910    :meth:`Reader`.
1911
1912    See :ref:`Writing a Import Routine<Import_Routines>`
1913    for an explanation on how to use import classes in general. The specifics
1914    for reading a structure factor histogram require that
1915    the ``Reader()`` routine in the import
1916    class need to do only a few things: It
1917    should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1918    and set :attr:`Parameters` with the instrument parameters
1919    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1920    '''
1921    def __init__(self,formatName,longFormatName=None,extensionlist=[],
1922        strictExtension=False,):
1923        ImportBaseclass.__init__(self,formatName,longFormatName,
1924            extensionlist,strictExtension)
1925
1926        # define contents of Structure Factor entry
1927        self.Parameters = []
1928        'self.Parameters is a list with two dicts for data parameter settings'
1929        self.InitParameters()
1930        self.RefDict = {'RefList':[],'FF':{},'Super':0}
1931        self.Banks = []             #for multi bank data (usually TOF)
1932        '''self.RefDict is a dict containing the reflection information, as read from the file.
1933        Item 'RefList' contains the reflection information. See the
1934        :ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1935        for the contents of each row. Dict element 'FF'
1936        contains the form factor values for each element type; if this entry
1937        is left as initialized (an empty list) it will be initialized as needed later.
1938        '''
1939    def ReInitialize(self):
1940        'Reinitialize the Reader to initial settings'
1941        ImportBaseclass.ReInitialize(self)
1942        self.InitParameters()
1943        self.Banks = []             #for multi bank data (usually TOF)
1944        self.RefDict = {'RefList':[],'FF':{},'Super':0}
1945       
1946    def InitParameters(self):
1947        'initialize the instrument parameters structure'
1948        Lambda = 0.70926
1949        HistType = 'SXC'
1950        self.Parameters = [{'Type':[HistType,HistType], # create the structure
1951                            'Lam':[Lambda,Lambda]
1952                            }, {}]
1953        'Parameters is a list with two dicts for data parameter settings'
1954
1955    def UpdateParameters(self,Type=None,Wave=None):
1956        'Revise the instrument parameters'
1957        if Type is not None:
1958            self.Parameters[0]['Type'] = [Type,Type]
1959        if Wave is not None:
1960            self.Parameters[0]['Lam'] = [Wave,Wave]           
1961                       
1962######################################################################
1963class ImportPowderData(ImportBaseclass):
1964    '''Defines a base class for the reading of files with powder data.
1965
1966    Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1967    in :meth:`GSASIIdataGUI.GSASII.OnImportPowder`.
1968    See :ref:`Writing a Import Routine<Import_Routines>`
1969    for an explanation on how to use this class.
1970    '''
1971    def __init__(self,formatName,longFormatName=None,
1972        extensionlist=[],strictExtension=False,):
1973        ImportBaseclass.__init__(self,formatName,longFormatName,
1974            extensionlist,strictExtension)
1975        self.clockWd = None  # used in TOF
1976        self.ReInitialize()
1977       
1978    def ReInitialize(self):
1979        'Reinitialize the Reader to initial settings'
1980        ImportBaseclass.ReInitialize(self)
1981        self.powderentry = ['',None,None] #  (filename,Pos,Bank)
1982        self.powderdata = [] # Powder dataset
1983        '''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1984                np.array(x), # x-axis values
1985                np.array(y), # powder pattern intensities
1986                np.array(w), # 1/sig(intensity)^2 values (weights)
1987                np.array(yc), # calc. intensities (zero)
1988                np.array(yb), # calc. background (zero)
1989                np.array(yd), # obs-calc profiles
1990        '''                           
1991        self.comments = []
1992        self.idstring = ''
1993        self.Sample = SetDefaultSample() # default sample parameters
1994        self.Controls = {}  # items to be placed in top-level Controls
1995        self.GSAS = None     # used in TOF
1996        self.repeat_instparm = True # Should a parm file be
1997        #                             used for multiple histograms?
1998        self.instparm = None # name hint from file of instparm to use
1999        self.instfile = '' # full path name to instrument parameter file
2000        self.instbank = '' # inst parm bank number
2001        self.instmsg = ''  # a label that gets printed to show
2002                           # where instrument parameters are from
2003        self.numbanks = 1
2004        self.instdict = {} # place items here that will be transferred to the instrument parameters
2005        self.pwdparms = {} # place parameters that are transferred directly to the tree
2006                           # here (typically from an existing GPX file)
2007######################################################################
2008class ImportSmallAngleData(ImportBaseclass):
2009    '''Defines a base class for the reading of files with small angle data.
2010    See :ref:`Writing a Import Routine<Import_Routines>`
2011    for an explanation on how to use this class.
2012    '''
2013    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2014        strictExtension=False,):
2015           
2016        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2017            strictExtension)
2018        self.ReInitialize()
2019       
2020    def ReInitialize(self):
2021        'Reinitialize the Reader to initial settings'
2022        ImportBaseclass.ReInitialize(self)
2023        self.smallangleentry = ['',None,None] #  (filename,Pos,Bank)
2024        self.smallangledata = [] # SASD dataset
2025        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2026                np.array(x), # x-axis values
2027                np.array(y), # powder pattern intensities
2028                np.array(w), # 1/sig(intensity)^2 values (weights)
2029                np.array(yc), # calc. intensities (zero)
2030                np.array(yd), # obs-calc profiles
2031                np.array(yb), # preset bkg
2032        '''                           
2033        self.comments = []
2034        self.idstring = ''
2035        self.Sample = SetDefaultSample()
2036        self.GSAS = None     # used in TOF
2037        self.clockWd = None  # used in TOF
2038        self.numbanks = 1
2039        self.instdict = {} # place items here that will be transferred to the instrument parameters
2040
2041######################################################################
2042class ImportReflectometryData(ImportBaseclass):
2043    '''Defines a base class for the reading of files with reflectometry data.
2044    See :ref:`Writing a Import Routine<Import_Routines>`
2045    for an explanation on how to use this class.
2046    '''
2047    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2048        strictExtension=False,):
2049           
2050        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2051            strictExtension)
2052        self.ReInitialize()
2053       
2054    def ReInitialize(self):
2055        'Reinitialize the Reader to initial settings'
2056        ImportBaseclass.ReInitialize(self)
2057        self.reflectometryentry = ['',None,None] #  (filename,Pos,Bank)
2058        self.reflectometrydata = [] # SASD dataset
2059        '''A small angle data set is a list with items [x,y,w,yc,yd]:
2060                np.array(x), # x-axis values
2061                np.array(y), # powder pattern intensities
2062                np.array(w), # 1/sig(intensity)^2 values (weights)
2063                np.array(yc), # calc. intensities (zero)
2064                np.array(yd), # obs-calc profiles
2065                np.array(yb), # preset bkg
2066        '''                           
2067        self.comments = []
2068        self.idstring = ''
2069        self.Sample = SetDefaultSample()
2070        self.GSAS = None     # used in TOF
2071        self.clockWd = None  # used in TOF
2072        self.numbanks = 1
2073        self.instdict = {} # place items here that will be transferred to the instrument parameters
2074
2075######################################################################
2076class ImportPDFData(ImportBaseclass):
2077    '''Defines a base class for the reading of files with PDF G(R) data.
2078    See :ref:`Writing a Import Routine<Import_Routines>`
2079    for an explanation on how to use this class.
2080    '''
2081    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2082        strictExtension=False,):
2083           
2084        ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2085            strictExtension)
2086        self.ReInitialize()
2087       
2088    def ReInitialize(self):
2089        'Reinitialize the Reader to initial settings'
2090        ImportBaseclass.ReInitialize(self)
2091        self.pdfentry = ['',None,None] #  (filename,Pos,Bank)
2092        self.pdfdata = [] # PDF G(R) dataset
2093        '''A pdf g(r) data set is a list with items [x,y]:
2094                np.array(x), # r-axis values
2095                np.array(y), # pdf g(r)
2096        '''                           
2097        self.comments = []
2098        self.idstring = ''
2099        self.numbanks = 1
2100
2101######################################################################
2102class ImportImage(ImportBaseclass):
2103    '''Defines a base class for the reading of images
2104
2105    Images are read in only these places:
2106   
2107      * Initial reading is typically done from a menu item
2108        with a call to :meth:`GSASIIdataGUI.GSASII.OnImportImage`
2109        which in turn calls :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`. That calls
2110        methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2111        :meth:`Reader`. This returns a list of reader objects for each read image.
2112
2113      * Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
2114        directly into the data tree.
2115
2116      * Images are reloaded with :func:`GSASIIIO.GetImageData`.
2117
2118    .. _Image_import_routines:
2119
2120    When reading an image, the ``Reader()`` routine in the ImportImage class
2121    should set:
2122   
2123      * :attr:`Comments`: a list of strings (str),
2124      * :attr:`Npix`: the number of pixels in the image (int),
2125      * :attr:`Image`: the actual image as a numpy array (np.array)
2126      * :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
2127        data items are needed:
2128       
2129         * 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
2130         * 'wavelength': wavelength in Angstoms.
2131         * 'distance': distance of detector from sample in cm.
2132         * 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
2133         * 'size': size of image (such as ``[2048,2048]``).
2134         * 'ImageTag': image number or other keyword used to retrieve image from
2135           a multi-image data file (defaults to ``1`` if not specified).
2136         * 'sumfile': holds sum image file name if a sum was produced from a multi image file
2137
2138    optional data items:
2139   
2140      * :attr:`repeat`: set to True if there are additional images to
2141        read in the file, False otherwise
2142      * :attr:`repeatcount`: set to the number of the image.
2143     
2144    Note that the above is initialized with :meth:`InitParameters`.
2145    (Also see :ref:`Writing a Import Routine<Import_Routines>`
2146    for an explanation on how to use import classes in general.)
2147    '''
2148    def __init__(self,formatName,longFormatName=None,extensionlist=[],
2149        strictExtension=False,):
2150        ImportBaseclass.__init__(self,formatName,longFormatName,
2151            extensionlist,strictExtension)
2152        self.InitParameters()
2153       
2154    def ReInitialize(self):
2155        'Reinitialize the Reader to initial settings -- not used at present'
2156        ImportBaseclass.ReInitialize(self)
2157        self.InitParameters()
2158       
2159    def InitParameters(self):
2160        'initialize the instrument parameters structure'
2161        self.Comments = ['No comments']
2162        self.Data = {}
2163        self.Npix = 0
2164        self.Image = None
2165        self.repeat = False
2166        self.repeatcount = 1
2167        self.sumfile = ''
2168
2169    def LoadImage(self,ParentFrame,imagefile,imagetag=None):
2170        '''Optionally, call this after reading in an image to load it into the tree.
2171        This saves time by preventing a reread of the same information.
2172        '''
2173        if ParentFrame:
2174            ParentFrame.ImageZ = self.Image   # store the image for plotting
2175            ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2176            ParentFrame.oldImageTag = imagetag   # save the tag of the last image file read           
2177
2178#################################################################################################
2179# shortcut routines
2180exp = np.exp
2181sind = sin = s = lambda x: np.sin(x*np.pi/180.)
2182cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
2183tand = tan = t = lambda x: np.tan(x*np.pi/180.)
2184sqrt = sq = lambda x: np.sqrt(x)
2185pi = lambda: np.pi
2186class ExpressionObj(object):
2187    '''Defines an object with a user-defined expression, to be used for
2188    secondary fits or restraints. Object is created null, but is changed
2189    using :meth:`LoadExpression`. This contains only the minimum
2190    information that needs to be stored to save and load the expression
2191    and how it is mapped to GSAS-II variables.
2192    '''
2193    def __init__(self):
2194        self.expression = ''
2195        'The expression as a text string'
2196        self.assgnVars = {}
2197        '''A dict where keys are label names in the expression mapping to a GSAS-II
2198        variable. The value a G2 variable name.
2199        Note that the G2 variable name may contain a wild-card and correspond to
2200        multiple values.
2201        '''
2202        self.freeVars = {}
2203        '''A dict where keys are label names in the expression mapping to a free
2204        parameter. The value is a list with:
2205
2206         * a name assigned to the parameter
2207         * a value for to the parameter and
2208         * a flag to determine if the variable is refined.
2209        ''' 
2210        self.depVar = None
2211
2212        self.lastError = ('','')
2213        '''Shows last encountered error in processing expression
2214        (list of 1-3 str values)'''
2215
2216        self.distance_dict  = None  # to be used for defining atom phase/symmetry info
2217        self.distance_atoms = None  # to be used for defining atom distances
2218
2219    def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
2220        '''Load the expression and associated settings into the object. Raises
2221        an exception if the expression is not parsed, if not all functions
2222        are defined or if not all needed parameter labels in the expression
2223        are defined.
2224
2225        This will not test if the variable referenced in these definitions
2226        are actually in the parameter dictionary. This is checked when the
2227        computation for the expression is done in :meth:`SetupCalc`.
2228       
2229        :param str expr: the expression
2230        :param list exprVarLst: parameter labels found in the expression
2231        :param dict varSelect: this will be 0 for Free parameters
2232          and non-zero for expression labels linked to G2 variables.
2233        :param dict varName: Defines a name (str) associated with each free parameter
2234        :param dict varValue: Defines a value (float) associated with each free parameter
2235        :param dict varRefflag: Defines a refinement flag (bool)
2236          associated with each free parameter
2237        '''
2238        self.expression = expr
2239        self.compiledExpr = None
2240        self.freeVars = {}
2241        self.assgnVars = {}
2242        for v in exprVarLst:
2243            if varSelect[v] == 0:
2244                self.freeVars[v] = [
2245                    varName.get(v),
2246                    varValue.get(v),
2247                    varRefflag.get(v),
2248                    ]
2249            else:
2250                self.assgnVars[v] = varName[v]
2251        self.CheckVars()
2252
2253    def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
2254        '''Load the expression and associated settings from the object into
2255        arrays used for editing.
2256
2257        :param list exprVarLst: parameter labels found in the expression
2258        :param dict varSelect: this will be 0 for Free parameters
2259          and non-zero for expression labels linked to G2 variables.
2260        :param dict varName: Defines a name (str) associated with each free parameter
2261        :param dict varValue: Defines a value (float) associated with each free parameter
2262        :param dict varRefflag: Defines a refinement flag (bool)
2263          associated with each free parameter
2264
2265        :returns: the expression as a str
2266        '''
2267        for v in self.freeVars:
2268            varSelect[v] = 0
2269            varName[v] = self.freeVars[v][0]
2270            varValue[v] = self.freeVars[v][1]
2271            varRefflag[v] = self.freeVars[v][2]
2272        for v in self.assgnVars:
2273            varSelect[v] = 1
2274            varName[v] = self.assgnVars[v]
2275        return self.expression
2276
2277    def GetVaried(self):
2278        'Returns the names of the free parameters that will be refined'
2279        return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
2280
2281    def GetVariedVarVal(self):
2282        'Returns the names and values of the free parameters that will be refined'
2283        return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
2284
2285    def UpdateVariedVars(self,varyList,values):
2286        'Updates values for the free parameters (after a refinement); only updates refined vars'
2287        for v in self.freeVars:
2288            if not self.freeVars[v][2]: continue
2289            if "::"+self.freeVars[v][0] not in varyList: continue
2290            indx = varyList.index("::"+self.freeVars[v][0])
2291            self.freeVars[v][1] = values[indx]
2292
2293    def GetIndependentVars(self):
2294        'Returns the names of the required independent parameters used in expression'
2295        return [self.assgnVars[v] for v in self.assgnVars]
2296
2297    def CheckVars(self):
2298        '''Check that the expression can be parsed, all functions are
2299        defined and that input loaded into the object is internally
2300        consistent. If not an Exception is raised.
2301
2302        :returns: a dict with references to packages needed to
2303          find functions referenced in the expression.
2304        '''
2305        ret = self.ParseExpression(self.expression)
2306        if not ret:
2307            raise Exception("Expression parse error")
2308        exprLblList,fxnpkgdict = ret
2309        # check each var used in expression is defined
2310        defined = self.assgnVars.keys() + self.freeVars.keys()
2311        notfound = []
2312        for var in exprLblList:
2313            if var not in defined:
2314                notfound.append(var)
2315        if notfound:
2316            msg = 'Not all variables defined'
2317            msg1 = 'The following variables were not defined: '
2318            msg2 = ''
2319            for var in notfound:
2320                if msg: msg += ', '
2321                msg += var
2322            self.lastError = (msg1,'  '+msg2)
2323            raise Exception(msg)
2324        return fxnpkgdict
2325
2326    def ParseExpression(self,expr):
2327        '''Parse an expression and return a dict of called functions and
2328        the variables used in the expression. Returns None in case an error
2329        is encountered. If packages are referenced in functions, they are loaded
2330        and the functions are looked up into the modules global
2331        workspace.
2332       
2333        Note that no changes are made to the object other than
2334        saving an error message, so that this can be used for testing prior
2335        to the save.
2336
2337        :returns: a list of used variables
2338        '''
2339        self.lastError = ('','')
2340        import ast
2341        def FindFunction(f):
2342            '''Find the object corresponding to function f
2343            :param str f: a function name such as 'numpy.exp'
2344            :returns: (pkgdict,pkgobj) where pkgdict contains a dict
2345              that defines the package location(s) and where pkgobj
2346              defines the object associated with the function.
2347              If the function is not found, pkgobj is None.
2348            '''
2349            df = f.split('.')
2350            pkgdict = {}
2351            # no listed package, try in current namespace
2352            if len(df) == 1: 
2353                try:
2354                    fxnobj = eval(f)
2355                    return pkgdict,fxnobj
2356                except (AttributeError, NameError):
2357                    return None,None
2358            else:
2359                try:
2360                    fxnobj = eval(f)
2361                    pkgdict[df[0]] = eval(df[0])
2362                    return pkgdict,fxnobj
2363                except (AttributeError, NameError):
2364                    pass
2365            # includes a package, lets try to load the packages
2366            pkgname = ''
2367            path = sys.path
2368            for pkg in f.split('.')[:-1]: # if needed, descend down the tree
2369                if pkgname:
2370                    pkgname += '.' + pkg
2371                else:
2372                    pkgname = pkg
2373                fp = None
2374                try:
2375                    fp, fppath,desc = imp.find_module(pkg,path)
2376                    pkgobj = imp.load_module(pkg,fp,fppath,desc)
2377                    pkgdict[pkgname] = pkgobj
2378                    path = [fppath]
2379                except Exception as msg:
2380                    print('load of '+pkgname+' failed with error='+str(msg))
2381                    return {},None
2382                finally:
2383                    if fp: fp.close()
2384                try:
2385                    #print 'before',pkgdict.keys()
2386                    fxnobj = eval(f,globals(),pkgdict)
2387                    #print 'after 1',pkgdict.keys()
2388                    #fxnobj = eval(f,pkgdict)
2389                    #print 'after 2',pkgdict.keys()
2390                    return pkgdict,fxnobj
2391                except:
2392                    continue
2393            return None # not found
2394        def ASTtransverse(node,fxn=False):
2395            '''Transverse a AST-parsed expresson, compiling a list of variables
2396            referenced in the expression. This routine is used recursively.
2397
2398            :returns: varlist,fxnlist where
2399              varlist is a list of referenced variable names and
2400              fxnlist is a list of used functions
2401            '''
2402            varlist = []
2403            fxnlist = []
2404            if isinstance(node, list):
2405                for b in node:
2406                    v,f = ASTtransverse(b,fxn)
2407                    varlist += v
2408                    fxnlist += f
2409            elif isinstance(node, ast.AST):
2410                for a, b in ast.iter_fields(node):
2411                    if isinstance(b, ast.AST):
2412                        if a == 'func': 
2413                            fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
2414                            continue
2415                        v,f = ASTtransverse(b,fxn)
2416                        varlist += v
2417                        fxnlist += f
2418                    elif isinstance(b, list):
2419                        v,f = ASTtransverse(b,fxn)
2420                        varlist += v
2421                        fxnlist += f
2422                    elif node.__class__.__name__ == "Name":
2423                        varlist += [b]
2424                    elif fxn and node.__class__.__name__ == "Attribute":
2425                        varlist += [b]
2426            return varlist,fxnlist
2427        try:
2428            exprast = ast.parse(expr)
2429        except SyntaxError:
2430            s = ''
2431            import traceback
2432            for i in traceback.format_exc().splitlines()[-3:-1]:
2433                if s: s += "\n"
2434                s += str(i)
2435            self.lastError = ("Error parsing expression:",s)
2436            return
2437        # find the variables & functions
2438        v,f = ASTtransverse(exprast)
2439        varlist = sorted(list(set(v)))
2440        fxnlist = list(set(f))
2441        pkgdict = {}
2442        # check the functions are defined
2443        for fxn in fxnlist:
2444            fxndict,fxnobj = FindFunction(fxn)
2445            if not fxnobj:
2446                self.lastError = ("Error: Invalid function",fxn,
2447                                  "is not defined")
2448                return
2449            if not hasattr(fxnobj,'__call__'):
2450                self.lastError = ("Error: Not a function.",fxn,
2451                                  "cannot be called as a function")
2452                return
2453            pkgdict.update(fxndict)
2454        return varlist,pkgdict
2455
2456    def GetDepVar(self):
2457        'return the dependent variable, or None'
2458        return self.depVar
2459
2460    def SetDepVar(self,var):
2461        'Set the dependent variable, if used'
2462        self.depVar = var
2463#==========================================================================
2464class ExpressionCalcObj(object):
2465    '''An object used to evaluate an expression from a :class:`ExpressionObj`
2466    object.
2467   
2468    :param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
2469      an expression string and mappings for the parameter labels in that object.
2470    '''
2471    def __init__(self,exprObj):
2472        self.eObj = exprObj
2473        'The expression and mappings; a :class:`ExpressionObj` object'
2474        self.compiledExpr = None
2475        'The expression as compiled byte-code'
2476        self.exprDict = {}
2477        '''dict that defines values for labels used in expression and packages
2478        referenced by functions
2479        '''
2480        self.lblLookup = {}
2481        '''Lookup table that specifies the expression label name that is
2482        tied to a particular GSAS-II parameters in the parmDict.
2483        '''
2484        self.fxnpkgdict = {}
2485        '''a dict with references to packages needed to
2486        find functions referenced in the expression.
2487        '''
2488        self.varLookup = {}
2489        '''Lookup table that specifies the GSAS-II variable(s)
2490        indexed by the expression label name. (Used for only for diagnostics
2491        not evaluation of expression.)
2492        '''
2493        self.su = None
2494        '''Standard error evaluation where supplied by the evaluator
2495        '''
2496        # Patch: for old-style expressions with a (now removed step size)
2497        for v in self.eObj.assgnVars:
2498            if not isinstance(self.eObj.assgnVars[v], basestring):
2499                self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
2500        self.parmDict = {}
2501        '''A copy of the parameter dictionary, for distance and angle computation
2502        '''
2503
2504    def SetupCalc(self,parmDict):
2505        '''Do all preparations to use the expression for computation.
2506        Adds the free parameter values to the parameter dict (parmDict).
2507        '''
2508        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2509            return
2510        self.fxnpkgdict = self.eObj.CheckVars()
2511        # all is OK, compile the expression
2512        self.compiledExpr = compile(self.eObj.expression,'','eval')
2513
2514        # look at first value in parmDict to determine its type
2515        parmsInList = True
2516        for key in parmDict:
2517            val = parmDict[key]
2518            if isinstance(val, basestring):
2519                parmsInList = False
2520                break
2521            try: # check if values are in lists
2522                val = parmDict[key][0]
2523            except (TypeError,IndexError):
2524                parmsInList = False
2525            break
2526           
2527        # set up the dicts needed to speed computations
2528        self.exprDict = {}
2529        self.lblLookup = {}
2530        self.varLookup = {}
2531        for v in self.eObj.freeVars:
2532            varname = self.eObj.freeVars[v][0]
2533            varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
2534            self.lblLookup[varname] = v
2535            self.varLookup[v] = varname
2536            if parmsInList:
2537                parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
2538            else:
2539                parmDict[varname] = self.eObj.freeVars[v][1]
2540            self.exprDict[v] = self.eObj.freeVars[v][1]
2541        for v in self.eObj.assgnVars:
2542            varname = self.eObj.assgnVars[v]
2543            if '*' in varname:
2544                varlist = LookupWildCard(varname,parmDict.keys())
2545                if len(varlist) == 0:
2546                    raise Exception,"No variables match "+str(v)
2547                for var in varlist:
2548                    self.lblLookup[var] = v
2549                if parmsInList:
2550                    self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
2551                else:
2552                    self.exprDict[v] = np.array([parmDict[var] for var in varlist])
2553                self.varLookup[v] = [var for var in varlist]
2554            elif varname in parmDict:
2555                self.lblLookup[varname] = v
2556                self.varLookup[v] = varname
2557                if parmsInList:
2558                    self.exprDict[v] = parmDict[varname][0]
2559                else:
2560                    self.exprDict[v] = parmDict[varname]
2561            else:
2562                self.exprDict[v] = None
2563#                raise Exception,"No value for variable "+str(v)
2564        self.exprDict.update(self.fxnpkgdict)
2565
2566    def UpdateVars(self,varList,valList):
2567        '''Update the dict for the expression with a set of values
2568        :param list varList: a list of variable names
2569        :param list valList: a list of corresponding values
2570        '''
2571        for var,val in zip(varList,valList):
2572            self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
2573
2574    def UpdateDict(self,parmDict):
2575        '''Update the dict for the expression with values in a dict
2576        :param list parmDict: a dict of values some of which may be in use here
2577        '''
2578        if self.eObj.expression.startswith('Dist') or self.eObj.expression.startswith('Angle'):
2579            self.parmDict = parmDict
2580            return
2581        for var in parmDict:
2582            if var in self.lblLookup:
2583                self.exprDict[self.lblLookup[var]] = parmDict[var]
2584           
2585    def EvalExpression(self):
2586        '''Evaluate an expression. Note that the expression
2587        and mapping are taken from the :class:`ExpressionObj` expression object
2588        and the parameter values were specified in :meth:`SetupCalc`.
2589        :returns: a single value for the expression. If parameter
2590        values are arrays (for example, from wild-carded variable names),
2591        the sum of the resulting expression is returned.
2592
2593        For example, if the expression is ``'A*B'``,
2594        where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
2595
2596        [0.5, 1, 0.5]
2597
2598        then the result will be ``4.0``.
2599        '''
2600        self.su = None
2601        if self.eObj.expression.startswith('Dist'):
2602#            GSASIIpath.IPyBreak()
2603            dist = G2mth.CalcDist(self.eObj.distance_dict, self.eObj.distance_atoms, self.parmDict)
2604            return dist
2605        elif self.eObj.expression.startswith('Angle'):
2606            angle = G2mth.CalcAngle(self.eObj.angle_dict, self.eObj.angle_atoms, self.parmDict)
2607            return angle
2608        if self.compiledExpr is None:
2609            raise Exception,"EvalExpression called before SetupCalc"
2610        try:
2611            val = eval(self.compiledExpr,globals(),self.exprDict)
2612        except TypeError:
2613            val = None
2614        if not np.isscalar(val):
2615            val = np.sum(val)
2616        return val
2617       
2618class G2Exception(Exception):
2619    def __init__(self,msg):
2620        self.msg = msg
2621    def __str__(self):
2622        return repr(self.msg)
2623
2624def HowDidIgetHere(wherecalledonly=False):
2625    '''Show a traceback with calls that brought us to the current location.
2626    Used for debugging.
2627    '''
2628    import traceback
2629    if wherecalledonly:
2630        i = traceback.format_list(traceback.extract_stack()[:-1])[-2]
2631        print(i.strip().rstrip())
2632    else:
2633        print 70*'*'   
2634        for i in traceback.format_list(traceback.extract_stack()[:-1]): print(i.strip().rstrip())
2635        print 70*'*'   
2636               
2637def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
2638    '''Create and initialize a new set of PDF tree entries
2639
2640    :param Frame G2frame: main GSAS-II tree frame object
2641    :param str PWDRtree: name of PWDR to be used to create PDF item
2642    :param dict ElList: data structure with composition
2643    :param list Qlimits: Q limits to be used for computing the PDF
2644    :param float numAtm: no. atom in chemical formula
2645    :param float FltBkg: flat background value
2646    :param list PDFnames: previously used PDF names
2647   
2648    :returns: the Id of the newly created PDF entry
2649    '''
2650    PDFname = 'PDF '+PWDRtree[4:] # this places two spaces after PDF, which is needed is some places
2651    if PDFname in PDFnames:
2652        print('Skipping, entry already exists: '+PDFname)
2653        return None
2654    #PDFname = MakeUniqueLabel(PDFname,PDFnames)
2655    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=PDFname)
2656    Data = {
2657        'Sample':{'Name':PWDRtree,'Mult':1.0},
2658        'Sample Bkg.':{'Name':'','Mult':-1.0,'Refine':False},
2659        'Container':{'Name':'','Mult':-1.0,'Refine':False},
2660        'Container Bkg.':{'Name':'','Mult':-1.0},'ElList':ElList,
2661        'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0*numAtm,'Flat Bkg':FltBkg,
2662        'DetType':'Area detector','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':Qlimits,
2663        'Lorch':False,'BackRatio':0.0,'Rmax':100.,'noRing':False,'IofQmin':1.0,
2664        'I(Q)':[],'S(Q)':[],'F(Q)':[],'G(R)':[]}
2665    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Controls'),Data)
2666    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'),
2667        {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
2668    return Id       
2669
2670
2671if __name__ == "__main__":
2672    # test equation evaluation
2673    def showEQ(calcobj):
2674        print 50*'='
2675        print calcobj.eObj.expression,'=',calcobj.EvalExpression()
2676        for v in sorted(calcobj.varLookup):
2677            print "  ",v,'=',calcobj.exprDict[v],'=',calcobj.varLookup[v]
2678        # print '  Derivatives'
2679        # for v in calcobj.derivStep.keys():
2680        #     print '    d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
2681
2682    obj = ExpressionObj()
2683
2684    obj.expression = "A*np.exp(B)"
2685    obj.assgnVars =  {'B': '0::Afrac:1'}
2686    obj.freeVars =  {'A': [u'A', 0.5, True]}
2687    #obj.CheckVars()
2688    calcobj = ExpressionCalcObj(obj)
2689
2690    obj1 = ExpressionObj()
2691    obj1.expression = "A*np.exp(B)"
2692    obj1.assgnVars =  {'B': '0::Afrac:*'}
2693    obj1.freeVars =  {'A': [u'Free Prm A', 0.5, True]}
2694    #obj.CheckVars()
2695    calcobj1 = ExpressionCalcObj(obj1)
2696
2697    obj2 = ExpressionObj()
2698    obj2.distance_stuff = np.array([[0,1],[1,-1]])
2699    obj2.expression = "Dist(1,2)"
2700    GSASIIpath.InvokeDebugOpts()
2701    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
2702    calcobj2 = ExpressionCalcObj(obj2)
2703    calcobj2.SetupCalc(parmDict2)
2704    showEQ(calcobj2)
2705   
2706    parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
2707    print '\nDict = ',parmDict1
2708    calcobj.SetupCalc(parmDict1)
2709    showEQ(calcobj)
2710    calcobj1.SetupCalc(parmDict1)
2711    showEQ(calcobj1)
2712
2713    parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
2714    print 'Dict = ',parmDict2
2715    calcobj.SetupCalc(parmDict2)
2716    showEQ(calcobj)
2717    calcobj1.SetupCalc(parmDict2)
2718    showEQ(calcobj1)
2719    calcobj2.SetupCalc(parmDict2)
2720    showEQ(calcobj2)
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