source: trunk/GSASIIobj.py @ 1181

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bypass format bug, add histogram prms to parmDict, more docs

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1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2014-01-02 20:18:25 +0000 (Thu, 02 Jan 2014) $
5# $Author: toby $
6# $Revision: 1181 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 1181 2014-01-02 20:18:25Z toby $
9########### SVN repository information ###################
10
11'''
12*GSASIIobj: Data objects*
13=========================
14
15This module defines and/or documents the data structures used in GSAS-II, as well
16as provides misc. support routines.
17
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
360Atom Records
361------------
362
363.. _Atoms_table:
364
365.. index::
366   single: Atoms record description
367   single: Data object descriptions; Atoms record
368
369
370If ``phasedict`` points to the phase information in the data tree, then
371atoms are contained in a list of atom records (list) in
372``phasedict['Atoms']``. Also needed to read atom information
373are four pointers, ``cx,ct,cs,cia = phasedict['General']['atomPtrs']``,
374which define locations in the atom record, as shown below. Items shown are
375always present; additional ones for macromolecular phases are marked 'mm'
376
377.. tabularcolumns:: |l|p{4.5in}|
378
379==============   ====================================================
380location         explanation
381==============   ====================================================
382ct-4              mm - residue number (str)
383ct-3              mm - residue name (e.g. ALA) (str)
384ct-2              mm - chain label (str)
385ct-1              atom label (str)
386ct                atom type (str)
387ct+1              refinement flags; combination of 'F', 'X', 'U' (str)
388cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
389cs                site symmetry (str)
390cs+1              site multiplicity (int)
391cia               ADP flag: Isotropic ('I') or Anisotropic ('A')
392cia+1             Uiso (float)
393cia+2...cia+6     U11, U22, U33, U12, U13, U23 (6 floats)
394atom[-1]                unique atom identifier (int)
395==============   ====================================================
396
397Drawing Atom Records
398--------------------
399
400.. _Drawing_atoms_table:
401
402.. index::
403   single: Drawing atoms record description
404   single: Data object descriptions; Drawing atoms record
405
406
407If ``phasedict`` points to the phase information in the data tree, then
408drawing atoms are contained in a list of drawing atom records (list) in
409``phasedict['Drawing']['Atoms']``. Also needed to read atom information
410are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
411which define locations in the atom record, as shown below. Items shown are
412always present; additional ones for macromolecular phases are marked 'mm'
413
414.. tabularcolumns:: |l|p{4.5in}|
415
416==============   ====================================================
417location         explanation
418==============   ====================================================
419ct-4              mm - residue number (str)
420ct-3              mm - residue name (e.g. ALA) (str)
421ct-2              mm - chain label (str)
422ct-1              atom label (str)
423ct                atom type (str)
424cx,cx+1,cx+2      the x,y and z coordinates (3 floats)
425cs-1              Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str)
426cs                atom drawing style; e.g. 'balls & sticks' (str)
427cs+1              atom label style (e.g. 'name') (str)
428cs+2              atom color (RBG triplet) (int)
429cs+3              ADP flag: Isotropic ('I') or Anisotropic ('A')
430cs+4              Uiso (float)
431cs+5...cs+11      U11, U22, U33, U12, U13, U23 (6 floats)
432ci                unique atom identifier; matches source atom Id in Atom Records (int)
433==============   ====================================================
434
435Powder Diffraction Tree Items
436-----------------------------
437
438.. _Powder_table:
439
440.. index::
441   single: Powder data object description
442   single: Data object descriptions; Powder Data
443
444Every powder diffraction histogram is stored in the GSAS-II data tree
445with a top-level entry named beginning with the string "PWDR ". The
446diffraction data for that information are directly associated with
447that tree item and there are a series of children to that item. The
448routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
449and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
450load this information into a dictionary where the child tree name is
451used as a key, and the information in the main entry is assigned
452a key of ``Data``, as outlined below.
453
454.. tabularcolumns:: |l|l|p{4in}|
455
456======================  ===============  ====================================================
457  key                      sub-key        explanation
458======================  ===============  ====================================================
459Comments                      \           Text strings extracted from the original powder
460                                          data header. These cannot be changed by the user;
461                                          it may be empty.
462Limits                       \            A list of two two element lists, as [[Ld,Hd],[L,H]]
463                                          where L and Ld are the current and default lowest
464                                          two-theta value to be used and
465                                          where H and Hd are the current and default highest
466                                          two-theta value to be used.
467Reflection Lists              \           A dict with an entry for each phase in the
468                                          histogram. The contents of each dict item
469                                          is a dict containing reflections, as described in
470                                          the :ref:`Powder Reflections <PowderRefl_table>`
471                                          description.
472Instrument Parameters         \           A list containing two dicts where the possible
473                                          keys in each dict are listed below. The value
474                                          for each item is a list containing three values:
475                                          the initial value, the current value and a
476                                          refinement flag which can have a value of
477                                          True, False or 0 where 0 indicates a value that
478                                          cannot be refined. The first and second
479                                          values are floats unless otherwise noted.
480                                          Items in the first dict are noted as [1]
481\                         Lam             Specifies a wavelength in Angstroms [1]
482\                         Lam1            Specifies the primary wavelength in
483                                          Angstrom, when an alpha1, alpha2
484                                          source is used [1]
485\                         Lam2            Specifies the secondary wavelength in
486                                          Angstrom, when an alpha1, alpha2
487                                          source is used [1]
488                          I(L2)/I(L1)     Ratio of Lam2 to Lam1 [1]           
489\                         Type            Histogram type (str) [1]:
490                                           * 'PXC' for constant wavelength x-ray
491                                           * 'PNC' for constant wavelength neutron
492                                           * 'PNT' for time of flight neutron
493\                         Zero            Two-theta zero correction in *degrees* [1]
494\                         Azimuth         Azimuthal setting angle for data recorded
495                                          with differing setting angles [1]
496\                         U, V, W         Cagliotti profile coefficients
497                                          for Gaussian instrumental broadening, where the
498                                          FWHM goes as
499                                          :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
500\                         X, Y            Cauchy (Lorentzian) instrumental broadening
501                                          coefficients [1]
502\                         SH/L            Variant of the Finger-Cox-Jephcoat asymmetric
503                                          peak broadening ratio. Note that this is the
504                                          average between S/L and H/L where S is
505                                          sample height, H is the slit height and
506                                          L is the goniometer diameter. [1]
507\                         Polariz.        Polarization coefficient. [1]
508wtFactor                      \           A weighting factor to increase or decrease
509                                          the leverage of data in the histogram (float).
510                                          A value of 1.0 weights the data with their
511                                          standard uncertainties and a larger value
512                                          increases the weighting of the data (equivalent
513                                          to decreasing the uncertainties).
514Sample Parameters             \           Specifies a dict with parameters that describe how
515                                          the data were collected, as listed
516                                          below. Refinable parameters are a list containing
517                                          a float and a bool, where the second value
518                                          specifies if the value is refined, otherwise
519                                          the value is a float unless otherwise noted.
520\                         Scale           The histogram scale factor (refinable)
521\                         Absorption      The sample absorption coefficient as
522                                          :math:`\\mu r` where r is the radius
523                                          (refinable). Only valid for Debye-Scherrer geometry.
524\                         SurfaceRoughA   Surface roughness parameter A as defined by
525                                          Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable -
526                                          only valid for Bragg-Brentano geometry)                                         
527\                         SurfaceRoughB   Surface roughness parameter B (refinable -
528                                          only valid for Bragg-Brentano geometry)                                         
529\                         DisplaceX,      Sample displacement from goniometer center
530                          DisplaceY       where Y is along the beam direction and
531                                          X is perpendicular. Units are :math:`\\mu m`
532                                          (refinable).
533\                         Phi, Chi,       Goniometer sample setting angles, in degrees.
534                          Omega
535\                         Gonio. radius   Radius of the diffractometer in mm
536\                         InstrName       A name for the instrument, used in preparing
537                                          a CIF (str).
538\                         Force,          Variables that describe how the measurement
539                          Temperature,    was performed. Not used directly in
540                          Humidity,       any computations.
541                          Pressure,
542                          Voltage
543\                         ranId           The random-number Id for the histogram
544                                          (same value as where top-level key is ranId)
545\                         Type            Type of diffraction data, may be 'Debye-Scherrer'
546                                          or 'Bragg-Brentano' (str).
547\                         Diffuse         not in use?
548hId                           \           The number assigned to the histogram when
549                                          the project is loaded or edited (can change)
550ranId                         \           A random number id for the histogram
551                                          that does not change
552Background                    \           The background is stored as a list with where
553                                          the first item in the list is list and the second
554                                          item is a dict. The list contains the background
555                                          function and its coefficients; the dict contains
556                                          Debye diffuse terms and background peaks.
557                                          (TODO: this needs to be expanded.)
558Data                          \           The data consist of a list of 6 np.arrays
559                                          containing in order:
560
561                                           1. the x-postions (two-theta in degrees),
562                                           2. the intensity values (Yobs),
563                                           3. the weights for each Yobs value
564                                           4. the computed intensity values (Ycalc)
565                                           5. the background values
566                                           6. Yobs-Ycalc
567======================  ===============  ====================================================
568
569Powder Reflection Data Structure
570--------------------------------
571
572.. _PowderRefl_table:
573
574.. index::
575   single: Powder reflection object description
576   single: Data object descriptions; Powder Reflections
577   
578For every phase in a histogram, the ``Reflection Lists`` value is a dict
579one element of which is `'RefList'`, which is a np.array containing
580reflections. The columns in that array are documented below.
581
582==========  ====================================================
583  index         explanation
584==========  ====================================================
585 0,1,2       h,k,l (float)
586 3           multiplicity
587 4           d-space, Angstrom
588 5           pos, two-theta
589 6           sig, Gaussian width
590 7           gam, Lorenzian width
591 8           :math:`F_{obs}^2`
592 9           :math:`F_{calc}^2`
593 10          reflection phase, in degrees
594 11          intensity correction for reflection, this times
595             :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
596==========  ====================================================
597
598Single Crystal Tree Items
599-------------------------
600
601.. _Xtal_table:
602
603.. index::
604   single: Single Crystal data object description
605   single: Data object descriptions; Single crystal data
606
607Every single crystal diffraction histogram is stored in the GSAS-II data tree
608with a top-level entry named beginning with the string "HKLF ". The
609diffraction data for that information are directly associated with
610that tree item and there are a series of children to that item. The
611routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
612and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
613load this information into a dictionary where the child tree name is
614used as a key, and the information in the main entry is assigned
615a key of ``Data``, as outlined below.
616
617.. tabularcolumns:: |l|l|p{4in}|
618
619======================  ===============  ====================================================
620  key                      sub-key        explanation
621======================  ===============  ====================================================
622Data                          \           A dict that contains the
623                                          reflection table,
624                                          as described in the
625                                          :ref:`Single Crystal Reflections
626                                          <XtalRefl_table>`
627                                          description.
628
629Instrument Parameters         \           A list containing two dicts where the possible
630                                          keys in each dict are listed below. The value
631                                          for most items is a list containing two values:
632                                          the initial value, the current value.
633                                          The first and second
634                                          values are floats unless otherwise noted.
635\                         Lam             Specifies a wavelength in Angstroms (two floats)
636\                         Type            Histogram type (two str values):
637                                           * 'SXC' for constant wavelength x-ray
638                                           * 'SNC' for constant wavelength neutron
639                                           * 'SNT' for time of flight neutron
640\                         InstrName       A name for the instrument, used in preparing
641                                          a CIF (str).
642
643wtFactor                      \           A weighting factor to increase or decrease
644                                          the leverage of data in the histogram (float).
645                                          A value of 1.0 weights the data with their
646                                          standard uncertainties and a larger value
647                                          increases the weighting of the data (equivalent
648                                          to decreasing the uncertainties).
649
650hId                           \           The number assigned to the histogram when
651                                          the project is loaded or edited (can change)
652ranId                         \           A random number id for the histogram
653                                          that does not change
654======================  ===============  ====================================================
655
656Single Crystal Reflection Data Structure
657----------------------------------------
658
659.. _XtalRefl_table:
660
661.. index::
662   single: Single Crystal reflection object description
663   single: Data object descriptions; Single Crystal Reflections
664   
665For every single crystal a histogram, the ``'Data'`` item contains
666the structure factors as an np.array in item `'RefList'`.
667The columns in that array are documented below.
668
669==========  ====================================================
670  index         explanation
671==========  ====================================================
672 0,1,2       h,k,l (float)
673 3           multiplicity
674 4           d-space, Angstrom
675 5           :math:`F_{obs}^2`
676 6           :math:`\sigma(F_{obs}^2)`
677 7           :math:`F_{calc}^2`
678 8           :math:`F_{obs}^2T`
679 9           :math:`F_{calc}^2T`
680 10          reflection phase, in degrees
681 11          intensity correction for reflection, this times
682             :math:`F_{obs}^2` or :math:`F_{calc}^2`
683             gives Iobs or Icalc
684==========  ====================================================
685
686Image Data Structure
687--------------------
688
689.. _Image_table:
690
691.. index::
692   image: Image data object description
693   image: Image object descriptions
694   
695Every 2-dimensional image is stored in the GSAS-II data tree
696with a top-level entry named beginning with the string "IMG ". The
697image data are directly associated with that tree item and there
698are a series of children to that item. The routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
699and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
700load this information into a dictionary where the child tree name is
701used as a key, and the information in the main entry is assigned
702a key of ``Data``, as outlined below.
703
704.. tabularcolumns:: |l|l|p{4in}|
705
706======================  ======================  ====================================================
707  key                      sub-key              explanation
708======================  ======================  ====================================================
709Comments                       \                Text strings extracted from the original image data
710                                                header or a metafile. These cannot be changed by 
711                                                the user; it may be empty.                                               
712Image Controls              azmthOff            (float) The offset to be applied to an azimuthal
713                                                value. Accomodates
714                                                detector orientations other than with the detector
715                                                X-axis
716                                                horizontal.
717\                           background image    (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
718                                                during image integration multiplied by value. It must have the same size/shape as
719                                                the integrated image. NB: value < 0 for subtraction.
720\                           calibrant           (str) The material used for determining the position/orientation
721                                                of the image. The data is obtained from :func:`ImageCalibrants`
722                                                and UserCalibrants.py (supplied by user).
723\                           calibdmin           (float) The minimum d-spacing used during the last calibration run.
724\                           calibskip           (int) The number of expected diffraction lines skipped during the last
725                                                calibration run.
726\                           center              (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
727                                                strikes the detector plane as determined by calibration. This point
728                                                does not have to be within the limits of the detector boundaries.
729\                           centerAzm           (bool) If True then the azimuth reported for the integrated slice
730                                                of the image is at the center line otherwise it is at the leading edge.
731\                           color               (str) The name of the colormap used to display the image. Default = 'Paired'.
732\                           cutoff              (float) The minimum value of I/Ib for a point selected in a diffraction ring for
733                                                calibration calculations. See pixLimit for details as how point is found.           
734\                           DetDepth            (float) Coefficient for penetration correction to distance; accounts for diffraction
735                                                ring offset at higher angles. Optionally determined by calibration.
736\                           DetDepthRef         (bool) If True then refine DetDepth during calibration/recalibration calculation.
737\                           distance            (float) The distance (mm) from sample to detector plane.
738\                           ellipses            (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
739                                                center (list) is location (mm) of the ellipse center on the detector plane, phi is the
740                                                rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
741                                                radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
742                                                is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
743\                           edgemin             (float) Not used;  parameter in EdgeFinder code.
744\                           fullIntegrate       (bool) If True then integrate over full 360 deg azimuthal range.
745\                           GonioAngles         (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
746                                                Required for texture calculations.
747\                           invert_x            (bool) If True display the image with the x-axis inverted.
748\                           invert_y            (bool) If True display the image with the y-axis inverted.
749\                           IOtth               (list:floats) The minimum and maximum 2-theta values to be used for integration.
750\                           LRazimuth           (list:floats) The minimum and maximum azimuth values to be used for integration.
751\                           Oblique             (list:float,bool) If True apply a detector absorption correction using the value to the
752                                                intensities obtained during integration.
753\                           outAzimuths         (int) The number of azimuth pie slices.
754\                           outChannels         (int) The number of 2-theta steps.
755\                           pixelSize           (list:ints) The X,Y dimensions (microns) of each pixel.
756\                           pixLimit            (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
757                                                This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
758                                                and subject to cutoff in :func:`GSASIIimage.makeRing`.
759                                                Locations are used to construct rings of points for calibration calcualtions.
760\                           PolaVal             (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
761                                                integration using value.
762\                           rings               (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
763                                                diffraction ring with the same d-spacing (dsp)
764\                           ring                (list) The x,y coordinates of the >5 points on an inner ring
765                                                selected by the user,
766\                           Range               (list) The minimum & maximum values of the image
767\                           rotation            (float) The angle between the x-axis and the vector about which the
768                                                detector is tilted. Constrained to -180 to 180 deg.     
769\                           SampleShape         (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
770                                                calculations.
771\                           SampleAbs           (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
772                                                to cause correction to be applied.
773\                           setDefault          (bool) If True the use the image controls values for all new images to be read. (might be removed)
774\                           setRings            (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.           
775\                           showLines           (bool) If True then isplay the integration limits to be used.
776\                           size                (list:int) The number of pixels on the image x & y axes
777\                           type                (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
778\                           tilt                (float) The angle the detector normal makes with the incident beam; range -90 to 90.
779\                           wavelength          (float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).
780                                               
781Masks                       Arcs                (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
782                                                to be excluded from integration
783\                           Frames              (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
784                                                of which is excluded from recalibration and integration. Only one frame is allowed.
785\                           Points              (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
786                                                from integration.
787\                           Polygons            (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
788                                                to be excluded from integration.
789\                           Rings               (list: lists) Each entry [2-theta,thickness] describes a ring mask
790                                                to be excluded from integration.
791\                           Thresholds          (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
792                                                in integrsation. The tuple is the image intensity limits and the list are those set by the user.   
793                                               
794Stress/Strain               Sample phi          (float) Sample rotation about vertical axis.
795\                           Sample z            (float) Sample translation from the calibration sample position (for Sample phi = 0)
796\                           strain              (list: 3x3 array of float) The strain tensor coefficients [[' e11','e12','e13'],[' e21','e22','e23'],[' e31','e32','e33']].
797                                                These will be restricted by space group symmetry; result of strain fit refinement.
798\                           Type                (str) 'True' or 'Conventional': The strain model used for the calculation.
799\                           d-zero              (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase and are used to determine the strain tensor.
800                                                The dictionary items are:
801                                                'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
802                                                'Dcalc': (float) d-spacing...
803                                                'pixLimit': (int) Search range to find highest point on ring for each data point
804                                                'cutoff': (float) I/Ib cutoff for searching.
805                                                'ImxyObs': (list:lists) [[X],[Y]] observed points to be used for strain calculations.
806                                                'ImxyCalc':(list:lists) [[X],[Y]] calculated points based on refined strain.                                           
807                                               
808======================  ======================  ====================================================
809
810Parameter Dictionary
811-------------------------
812
813.. _parmDict_table:
814
815.. index::
816   single: Parameter dictionary
817
818The parameter dictionary contains all of the variable parameters for the refinement.
819The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
820It is prepared in two ways. When loaded from the tree
821(in :meth:`GSASII.GSASII.MakeLSParmDict` and
822:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
823the values are lists with two elements: ``[value, refine flag]``
824
825When loaded from the GPX file (in
826:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
827dict is the actual parameter value (usually a float, but sometimes a
828letter or string flag value (such as I or A for iso/anisotropic).
829
830
831*Classes and routines*
832----------------------
833
834'''
835import random as ran
836import sys
837import GSASIIpath
838import GSASIImath as G2mth
839
840GSASIIpath.SetVersionNumber("$Revision: 1181 $")
841
842DefaultControls = {
843    'deriv type':'analytic Hessian',    #default controls
844    'min dM/M':0.0001,'shift factor':1.,'max cyc':3,'F**2':True,
845    'minF/sig':0,
846    'Author':'no name',
847    'FreeVar1':'Sample humidity (%)',
848    'FreeVar2':'Sample voltage (V)',
849    'FreeVar3':'Applied load (MN)',
850    }
851'''Values to be used as defaults for the initial contents of the ``Controls``
852data tree item.
853'''
854
855def MakeUniqueLabel(lbl,labellist):
856    '''Make sure that every a label is unique against a list by adding
857    digits at the end until it is not found in list.
858
859    :param str lbl: the input label
860    :param list labellist: the labels that have already been encountered
861    :returns: lbl if not found in labellist or lbl with ``_1-9`` (or
862      ``_10-99``, etc.) appended at the end
863    '''
864    lbl = lbl.strip()
865    if not lbl: # deal with a blank label
866        lbl = '_1'
867    if lbl not in labellist:
868        labellist.append(lbl)
869        return lbl
870    i = 1
871    prefix = lbl
872    if '_' in lbl:
873        prefix = lbl[:lbl.rfind('_')]
874        suffix = lbl[lbl.rfind('_')+1:]
875        try:
876            i = int(suffix)+1
877        except: # suffix could not be parsed
878            i = 1
879            prefix = lbl
880    while prefix+'_'+str(i) in labellist:
881        i += 1
882    else:
883        lbl = prefix+'_'+str(i)
884        labellist.append(lbl)
885    return lbl
886
887PhaseIdLookup = {}
888'''dict listing phase name and random Id keyed by sequential phase index as a str;
889best to access this using :func:`LookupPhaseName`
890'''
891PhaseRanIdLookup = {}
892'''dict listing phase sequential index keyed by phase random Id;
893best to access this using :func:`LookupPhaseId`
894'''
895HistIdLookup = {}
896'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
897best to access this using :func:`LookupHistName`
898'''
899HistRanIdLookup = {}
900'''dict listing histogram sequential index keyed by histogram random Id;
901best to access this using :func:`LookupHistId`
902'''
903AtomIdLookup = {}
904'''dict listing for each phase index as a str, the atom label and atom random Id,
905keyed by atom sequential index as a str;
906best to access this using :func:`LookupAtomLabel`
907'''
908AtomRanIdLookup = {}
909'''dict listing for each phase the atom sequential index keyed by atom random Id;
910best to access this using :func:`LookupAtomId`
911'''
912ShortPhaseNames = {}
913'''a dict containing a possibly shortened and when non-unique numbered
914version of the phase name. Keyed by the phase sequential index.
915'''
916ShortHistNames = {}
917'''a dict containing a possibly shortened and when non-unique numbered
918version of the histogram name. Keyed by the histogram sequential index.
919'''
920
921VarDesc = {}
922''' This dictionary lists descriptions for GSAS-II variables,
923as set in :func:`CompileVarDesc`. See that function for a description
924for how keys and values are written.
925'''
926
927reVarDesc = {}
928''' This dictionary lists descriptions for GSAS-II variables with
929the same values as :attr:`VarDesc` except that keys have been compiled as
930regular expressions. Initialized in :func:`CompileVarDesc`.
931'''
932
933def IndexAllIds(Histograms,Phases):
934    '''Scan through the used phases & histograms and create an index
935    to the random numbers of phases, histograms and atoms. While doing this,
936    confirm that assigned random numbers are unique -- just in case lightning
937    strikes twice in the same place.
938
939    Note: this code assumes that the atom random Id (ranId) is the last
940    element each atom record.
941
942    This is called in two places (only) :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
943    (which loads the histograms and phases from a GPX file) and
944    :meth:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
945    (which loads the histograms and phases from the data tree.)
946
947    TODO: do we need a lookup for rigid body variables?
948    '''
949    # process phases and atoms
950    PhaseIdLookup.clear()
951    PhaseRanIdLookup.clear()   
952    AtomIdLookup.clear()
953    AtomRanIdLookup.clear()
954    ShortPhaseNames.clear()
955    for ph in Phases:
956        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
957        ranId = Phases[ph]['ranId'] 
958        while ranId in PhaseRanIdLookup:
959            # Found duplicate random Id! note and reassign
960            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
961            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxint)
962        pId = str(Phases[ph]['pId'])
963        PhaseIdLookup[pId] = (ph,ranId)
964        PhaseRanIdLookup[ranId] = pId
965        shortname = ph[:10]
966        while shortname in ShortPhaseNames.values():
967            shortname = ph[:8] + ' ('+ pId + ')'
968        ShortPhaseNames[pId] = shortname
969        AtomIdLookup[pId] = {}
970        AtomRanIdLookup[pId] = {}
971        for iatm,at in enumerate(Phases[ph]['Atoms']):
972            ranId = at[-1]
973            while ranId in AtomRanIdLookup[pId]: # check for dups
974                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
975                at[-1] = ranId = ran.randint(0,sys.maxint)
976            AtomRanIdLookup[pId][ranId] = str(iatm)
977            if Phases[ph]['General']['Type'] == 'macromolecular':
978                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
979            else:
980                label = at[ct-1]
981            AtomIdLookup[pId][str(iatm)] = (label,ranId)
982    # process histograms
983    HistIdLookup.clear()
984    HistRanIdLookup.clear()
985    ShortHistNames.clear()
986    for hist in Histograms:
987        ranId = Histograms[hist]['ranId']
988        while ranId in HistRanIdLookup:
989            # Found duplicate random Id! note and reassign
990            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
991            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxint)
992        hId = str(Histograms[hist]['hId'])
993        HistIdLookup[hId] = (hist,ranId)
994        HistRanIdLookup[ranId] = hId
995        shortname = hist[:15]
996        while shortname in ShortHistNames.values():
997            shortname = hist[:11] + ' ('+ hId + ')'
998        ShortHistNames[hId] = shortname
999
1000def LookupAtomId(pId,ranId):
1001    '''Get the atom number from a phase and atom random Id
1002
1003    :param int/str pId: the sequential number of the phase
1004    :param int ranId: the random Id assigned to an atom
1005
1006    :returns: the index number of the atom (str)
1007    '''
1008    if not AtomRanIdLookup:
1009        raise Exception,'Error: LookupAtomId called before IndexAllIds was run'
1010    if pId is None or pId == '':
1011        raise KeyError,'Error: phase is invalid (None or blank)'
1012    pId = str(pId)
1013    if pId not in AtomRanIdLookup:
1014        raise KeyError,'Error: LookupAtomId does not have phase '+pId
1015    if ranId not in AtomRanIdLookup[pId]:
1016        raise KeyError,'Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']'
1017    return AtomRanIdLookup[pId][ranId]
1018
1019def LookupAtomLabel(pId,index):
1020    '''Get the atom label from a phase and atom index number
1021
1022    :param int/str pId: the sequential number of the phase
1023    :param int index: the index of the atom in the list of atoms
1024
1025    :returns: the label for the atom (str) and the random Id of the atom (int)
1026    '''
1027    if not AtomIdLookup:
1028        raise Exception,'Error: LookupAtomLabel called before IndexAllIds was run'
1029    if pId is None or pId == '':
1030        raise KeyError,'Error: phase is invalid (None or blank)'
1031    pId = str(pId)
1032    if pId not in AtomIdLookup:
1033        raise KeyError,'Error: LookupAtomLabel does not have phase '+pId
1034    if index not in AtomIdLookup[pId]:
1035        raise KeyError,'Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']'
1036    return AtomIdLookup[pId][index]
1037
1038def LookupPhaseId(ranId):
1039    '''Get the phase number and name from a phase random Id
1040
1041    :param int ranId: the random Id assigned to a phase
1042    :returns: the sequential Id (pId) number for the phase (str)
1043    '''
1044    if not PhaseRanIdLookup:
1045        raise Exception,'Error: LookupPhaseId called before IndexAllIds was run'
1046    if ranId not in PhaseRanIdLookup:
1047        raise KeyError,'Error: LookupPhaseId does not have ranId '+str(ranId)
1048    return PhaseRanIdLookup[ranId]
1049
1050def LookupPhaseName(pId):
1051    '''Get the phase number and name from a phase Id
1052
1053    :param int/str pId: the sequential assigned to a phase
1054    :returns:  (phase,ranId) where phase is the name of the phase (str)
1055      and ranId is the random # id for the phase (int)
1056    '''
1057    if not PhaseIdLookup:
1058        raise Exception,'Error: LookupPhaseName called before IndexAllIds was run'
1059    if pId is None or pId == '':
1060        raise KeyError,'Error: phase is invalid (None or blank)'
1061    pId = str(pId)
1062    if pId not in PhaseIdLookup:
1063        raise KeyError,'Error: LookupPhaseName does not have index '+pId
1064    return PhaseIdLookup[pId]
1065
1066def LookupHistId(ranId):
1067    '''Get the histogram number and name from a histogram random Id
1068
1069    :param int ranId: the random Id assigned to a histogram
1070    :returns: the sequential Id (hId) number for the histogram (str)
1071    '''
1072    if not HistRanIdLookup:
1073        raise Exception,'Error: LookupHistId called before IndexAllIds was run'
1074    if ranId not in HistRanIdLookup:
1075        raise KeyError,'Error: LookupHistId does not have ranId '+str(ranId)
1076    return HistRanIdLookup[ranId]
1077
1078def LookupHistName(hId):
1079    '''Get the histogram number and name from a histogram Id
1080
1081    :param int/str hId: the sequential assigned to a histogram
1082    :returns:  (hist,ranId) where hist is the name of the histogram (str)
1083      and ranId is the random # id for the histogram (int)
1084    '''
1085    if not HistIdLookup:
1086        raise Exception,'Error: LookupHistName called before IndexAllIds was run'
1087    if hId is None or hId == '':
1088        raise KeyError,'Error: histogram is invalid (None or blank)'
1089    hId = str(hId)
1090    if hId not in HistIdLookup:
1091        raise KeyError,'Error: LookupHistName does not have index '+hId
1092    return HistIdLookup[hId]
1093
1094def fmtVarDescr(varname):
1095    '''Return a string with a more complete description for a GSAS-II variable
1096
1097    TODO: This will not handle rigid body parameters yet
1098
1099    :param str name: A full G2 variable name with 2 or 3
1100       colons (<p>:<h>:name[:<a>])
1101       
1102    :returns: a string with the description
1103    '''
1104   
1105    l = getVarDescr(varname)
1106    if not l:
1107        return "invalid variable name ("+str(varname)+")!"
1108
1109    if not l[4]:
1110        l[4] = "(variable needs a definition!)"
1111
1112    s = ""
1113    if l[0] is not None and l[1] is not None: # HAP: keep short
1114        lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
1115        hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1116        if hlbl[:4] == 'HKLF':
1117            hlbl = 'Xtl='+hlbl[5:]
1118        elif hlbl[:4] == 'PWDR':
1119            hlbl = 'Pwd='+hlbl[5:]
1120        else:
1121            hlbl = 'Hist='+hlbl
1122        s = "Ph="+str(lbl)+" * "+str(hlbl)+": "
1123    elif l[3] is not None: # atom parameter,
1124        lbl = ShortPhaseNames.get(l[0],'phase?')
1125        try:
1126            albl = LookupAtomLabel(l[0],l[3])[0]
1127        except KeyError:
1128            albl = 'Atom?'
1129        s = "Atom "+str(albl)+" in "+str(lbl)+": "
1130    elif l[0] is not None:
1131        lbl = ShortPhaseNames.get(l[0],'phase?')
1132        s = "Phase "+str(lbl)+": "
1133    elif l[1] is not None:
1134        hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
1135        if hlbl[:4] == 'HKLF':
1136            hlbl = 'Xtl='+hlbl[5:]
1137        elif hlbl[:4] == 'PWDR':
1138            hlbl = 'Pwd='+hlbl[5:]
1139        else:
1140            hlbl = 'Hist='+hlbl
1141        s = str(hlbl)+": "   
1142    if not s:
1143        s = 'Global: '
1144    s += l[4]
1145    return s
1146
1147def getVarDescr(varname):
1148    '''Return a short description for a GSAS-II variable
1149
1150    :param str name: A full G2 variable name with 2 or 3
1151       colons (<p>:<h>:name[:<a>])
1152     
1153    :returns: a five element list as [`p`,`h`,`name`,`a`,`description`],
1154      where `p`, `h`, `a` are str values or `None`, for the phase number,
1155      the histogram number and the atom number; `name` will always be
1156      an str; and `description` is str or `None`.
1157      If the variable name is incorrectly formed (for example, wrong
1158      number of colons), `None` is returned instead of a list.
1159    '''
1160    l = varname.split(':')
1161    if len(l) == 3:
1162        l += [None]
1163    if len(l) != 4:
1164        return None
1165    for i in (0,1,3):
1166        if l[i] == "":
1167            l[i] = None
1168    l += [getDescr(l[2])]
1169    return l
1170   
1171def CompileVarDesc():
1172    '''Set the values in the variable description lookup table (:attr:`VarDesc`)
1173    into :attr:`reVarDesc`. This is called in :func:`getDescr` so the initialization
1174    is always done before use.
1175
1176    Note that keys may contain regular expressions, where '[xyz]'
1177    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range of values).
1178    '.*' matches any string. For example::
1179
1180    'AUiso':'Atomic isotropic displacement parameter',
1181
1182    will match variable ``'p::AUiso:a'``.
1183    If parentheses are used in the key, the contents of those parentheses can be
1184    used in the value, such as::
1185
1186    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1187
1188    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1189    in the value when used.
1190   
1191    '''
1192    import re
1193    if reVarDesc: return # already done
1194    for key,value in {
1195        # Phase vars (p::<var>)
1196        'A([0-5])' : 'Reciprocal metric tensor component \\1',
1197        'Vol' : 'Unit cell volume????',
1198        # Atom vars (p::<var>:a)
1199        'dA([xyz])' : 'change to atomic position \\1',
1200        'AUiso':'Atomic isotropic displacement parameter',
1201        'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1202        'Afrac': 'Atomic occupancy parameter',
1203        # Hist & Phase (HAP) vars (p:h:<var>)
1204        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1205        'D([123][123])' : 'Anisotropic strain coef. \\1',
1206        'Extinction' : 'Extinction coef.',
1207        'MD' : 'March-Dollase coef.',
1208        'Mustrain;.*' : 'Microstrain coef.',
1209        'Scale' : 'Phase scale factor',
1210        'Size;.*' : 'Crystallite size value',
1211        'eA' : '?',
1212        #Histogram vars (:h:<var>)
1213        'Absorption' : 'Absorption coef.',
1214        'Displace([XY])' : 'Debye-Scherrer sample displacement \\1',
1215        'Lam' : 'Wavelength',
1216        'Polariz\.' : 'Polarization correction',
1217        'SH/L' : 'FCJ peak asymmetry correction',
1218        'Scale' : 'Histogram scale factor',
1219        '([UVW])' : 'Gaussian instrument broadening \\1',
1220        '([XY])' : 'Cauchy instrument broadening \\1',
1221        'Zero' : 'Debye-Scherrer zero correction',
1222        'nDebye' : 'Debye model background corr. terms',
1223        'nPeaks' : 'Fixed peak background corr. terms',
1224        # Global vars (::<var>)
1225        }.items():
1226        VarDesc[key] = value
1227        reVarDesc[re.compile(key)] = value
1228
1229def getDescr(name):
1230    '''Return a short description for a GSAS-II variable
1231
1232    :param str name: The descriptive part of the variable name without colons (:)
1233     
1234    :returns: a short description or None if not found
1235    '''
1236
1237    CompileVarDesc() # compile the regular expressions, if needed
1238    for key in reVarDesc:
1239        m = key.match(name)
1240        if m:
1241            return m.expand(reVarDesc[key])
1242    return None
1243
1244def _lookup(dic,key):
1245    '''Lookup a key in a dictionary, where None returns an empty string
1246    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
1247    '''
1248    if key is None:
1249        return ""
1250    else:
1251        return dic.get(key,'?')
1252
1253class G2VarObj(object):
1254    '''Defines a GSAS-II variable either using the phase/atom/histogram
1255    unique Id numbers or using a character string that specifies
1256    variables by phase/atom/histogram number (which can change).
1257    Note that :func:`LoadID` should be used to (re)load the current Ids
1258    before creating or later using the G2VarObj object.
1259
1260    A :class:`G2VarObj` object can be created with a single parameter:
1261   
1262    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
1263      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
1264
1265     * p is the phase number (which may be left blank);
1266     * h is the histogram number (which may be left blank);
1267     * a is the atom number (which may be left blank in which case the third colon is omitted).
1268
1269      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
1270      Phase, Histogram, and AtomID are None or are ranId values and VarName is a string.     
1271
1272    If four positional arguments are supplied, they are:
1273
1274    :param str/int phasenum: The number for the phase
1275    :param str/int histnum: The number for the histogram
1276    :param str varname: a single value can be used to create a :class:`G2VarObj`
1277    :param str/int atomnum: The number for the atom
1278   
1279    '''
1280    IDdict = {}
1281    IDdict['phases'] = {}
1282    IDdict['hists'] = {}
1283    IDdict['atoms'] = {}
1284    def __init__(self,*args):
1285        self.phase = None
1286        self.histogram = None
1287        self.name = ''
1288        self.atom = None
1289        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
1290            self.phase,self.histogram,self.name,self.atom = args[0]
1291        elif len(args) == 1 and ':' in args[0]:           
1292            lst = args[0].split(':')
1293            self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1294            self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1295            self.name = lst[2]
1296            if len(lst) > 3:
1297                self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
1298        elif len(args) == 4:
1299            self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
1300            self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
1301            self.name = args[2]
1302            self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
1303        else:
1304            raise Exception,"Incorrectly called GSAS-II parameter name"
1305
1306        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
1307
1308    def __str__(self):
1309        return self.varname()
1310
1311    def varname(self):
1312        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
1313        string (p:h:<var>:a) or (p:h:<var>)
1314
1315        :returns: the variable name as a str
1316        '''
1317        ph = _lookup(PhaseRanIdLookup,self.phase)
1318        hist = _lookup(HistRanIdLookup,self.histogram)
1319        s = (ph + ":" + hist + ":" + 
1320             str(self.name))
1321        if self.atom:
1322            if ph in AtomRanIdLookup:
1323                s += ":" + AtomRanIdLookup[ph].get(self.atom,'?')
1324            else:
1325                s += ":?"
1326        return s
1327   
1328    def __repr__(self):
1329        '''Return the detailed contents of the object
1330        '''
1331        s = "<"
1332        if self.phase is not None:
1333            ph =  _lookup(PhaseRanIdLookup,self.phase)
1334            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
1335        if self.histogram is not None:
1336            hist = _lookup(HistRanIdLookup,self.histogram)
1337            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
1338        if self.atom is not None:
1339            s += "Atom rId=" + str(self.atom)
1340            if ph in AtomRanIdLookup:
1341                s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
1342            else:
1343                s += " (#? -- not found!); "
1344        s += 'Variable name="' + str(self.name) + '">'
1345        return s+"("+self.varname()+")"
1346
1347    def __eq__(self, other):
1348        if type(other) is type(self):
1349            return (self.phase == other.phase and
1350                    self.histogram == other.histogram and
1351                    self.name == other.name and
1352                    self.atom == other.atom)
1353        return False
1354
1355    def _show(self):
1356        'For testing, shows the current lookup table'
1357        print 'phases', self.IDdict['phases']
1358        print 'hists', self.IDdict['hists']
1359        print 'atomDict', self.IDdict['atoms']
1360
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