source: trunk/GSASIIobj.py @ 1147

Last change on this file since 1147 was 1147, checked in by toby, 9 years ago

Complete initial ISODISPLACE implementation; mod. phase initialization; change atom pointer init.; rework parameter display window

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Author Revision URL Id
File size: 55.0 KB
Line 
1# -*- coding: utf-8 -*-
2#GSASIIobj - data objects for GSAS-II
3########### SVN repository information ###################
4# $Date: 2013-11-22 22:24:29 +0000 (Fri, 22 Nov 2013) $
5# $Author: toby $
6# $Revision: 1147 $
7# $URL: trunk/GSASIIobj.py $
8# $Id: GSASIIobj.py 1147 2013-11-22 22:24:29Z 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======================  ===============  ====================================================
459Limits                       \            A list of two two element lists, as [[Ld,Hd],[L,H]]
460                                          where L and Ld are the current and default lowest
461                                          two-theta value to be used and
462                                          where H and Hd are the current and default highest
463                                          two-theta value to be used.
464Reflection Lists              \           A dict with an entry for each phase in the
465                                          histogram. The contents of each dict item
466                                          is a dict containing reflections, as described in
467                                          the :ref:`Powder Reflections <PowderRefl_table>`
468                                          description.
469Instrument Parameters         \           A list containing two dicts where the possible
470                                          keys in each dict are listed below. The value
471                                          for each item is a list containing three values:
472                                          the initial value, the current value and a
473                                          refinement flag which can have a value of
474                                          True, False or 0 where 0 indicates a value that
475                                          cannot be refined. The first and second
476                                          values are floats unless otherwise noted.
477                                          Items in the first dict are noted as [1]
478\                         Lam             Specifies a wavelength in Angstroms [1]
479\                         Lam1            Specifies the primary wavelength in
480                                          Angstrom, when an alpha1, alpha2
481                                          source is used [1]
482\                         Lam2            Specifies the secondary wavelength in
483                                          Angstrom, when an alpha1, alpha2
484                                          source is used [1]
485                          I(L2)/I(L1)     Ratio of Lam2 to Lam1 [1]           
486\                         Type            Histogram type (str) [1]:
487                                           * 'PXC' for constant wavelength x-ray
488                                           * 'PNC' for constant wavelength neutron
489                                           * 'PNT' for time of flight neutron
490\                         Zero            Two-theta zero correction in *degrees* [1]
491\                         Azimuth         Azimuthal setting angle for data recorded
492                                          with differing setting angles [1]
493\                         U, V, W         Cagliotti profile coefficients
494                                          for Gaussian instrumental broadening, where the
495                                          FWHM goes as
496                                          :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
497\                         X, Y            Cauchy (Lorentzian) instrumental broadening
498                                          coefficients [1]
499\                         SH/L            Variant of the Finger-Cox-Jephcoat asymmetric
500                                          peak broadening ratio. Note that this is the
501                                          average between S/L and H/L where S is
502                                          sample height, H is the slit height and
503                                          L is the goniometer diameter. [1]
504\                         Polariz.        Polarization coefficient. [1]
505wtFactor                      \           A weighting factor to increase or decrease
506                                          the leverage of data in the histogram (float).
507                                          A value of 1.0 weights the data with their
508                                          standard uncertainties and a larger value
509                                          increases the weighting of the data (equivalent
510                                          to decreasing the uncertainties).
511Sample Parameters             \           Specifies a dict with parameters that describe how
512                                          the data were collected, as listed
513                                          below. Refinable parameters are a list containing
514                                          a float and a bool, where the second value
515                                          specifies if the value is refined, otherwise
516                                          the value is a float unless otherwise noted.
517\                         Scale           The histogram scale factor (refinable)
518\                         Absorption      The sample absorption coefficient as
519                                          :math:`\\mu r` where r is the radius
520                                          (refinable).
521\                         DisplaceX,      Sample displacement from goniometer center
522                          DisplaceY       where Y is along the beam direction and
523                                          X is perpendicular. Units are :math:`\\mu m`
524                                          (refinable).
525\                         Phi, Chi,       Goniometer sample setting angles, in degrees.
526                          Omega
527\                         Gonio. radius   Radius of the diffractometer in mm
528\                         InstrName       A name for the instrument, used in preparing
529                                          a CIF (str).
530\                         Force,          Variables that describe how the measurement
531                          Temperature,    was performed. Not used directly in
532                          Humidity,       any computations.
533                          Pressure,
534                          Voltage
535\                         ranId           The random-number Id for the histogram
536                                          (same value as where top-level key is ranId)
537\                         Type            Type of diffraction data, may be 'Debye-Scherrer'
538                                          or 'Bragg-Brentano' (str).
539\                         Diffuse         not in use?
540hId                           \           The number assigned to the histogram when
541                                          the project is loaded or edited (can change)
542ranId                         \           A random number id for the histogram
543                                          that does not change
544Background                    \           The background is stored as a list with where
545                                          the first item in the list is list and the second
546                                          item is a dict. The list contains the background
547                                          function and its coefficients; the dict contains
548                                          Debye diffuse terms and background peaks.
549                                          (TODO: this needs to be expanded.)
550Data                          \           The data consist of a list of 6 np.arrays
551                                          containing in order:
552
553                                           1. the x-postions (two-theta in degrees),
554                                           2. the intensity values (Yobs),
555                                           3. the weights for each Yobs value
556                                           4. the computed intensity values (Ycalc)
557                                           5. the background values
558                                           6. Yobs-Ycalc
559======================  ===============  ====================================================
560
561Powder Reflection Data Structure
562--------------------------------
563
564.. _PowderRefl_table:
565
566.. index::
567   single: Powder reflection object description
568   single: Data object descriptions; Powder Reflections
569   
570For every phase in a histogram, the ``Reflection Lists`` value is a dict
571one element of which is `'RefList'`, which is a np.array containing
572reflections. The columns in that array are documented below.
573
574==========  ====================================================
575  index         explanation
576==========  ====================================================
577 0,1,2       h,k,l (float)
578 3           multiplicity
579 4           d-space, Angstrom
580 5           pos, two-theta
581 6           sig, Gaussian width
582 7           gam, Lorenzian width
583 8           :math:`F_{obs}^2`
584 9           :math:`F_{calc}^2`
585 10          reflection phase, in degrees
586 11          intensity correction for reflection, this times
587             :math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
588==========  ====================================================
589
590Single Crystal Tree Items
591-------------------------
592
593.. _Xtal_table:
594
595.. index::
596   single: Single Crystal data object description
597   single: Data object descriptions; Single crystal data
598
599Every single crystal diffraction histogram is stored in the GSAS-II data tree
600with a top-level entry named beginning with the string "HKLF ". The
601diffraction data for that information are directly associated with
602that tree item and there are a series of children to that item. The
603routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
604and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
605load this information into a dictionary where the child tree name is
606used as a key, and the information in the main entry is assigned
607a key of ``Data``, as outlined below.
608
609.. tabularcolumns:: |l|l|p{4in}|
610
611======================  ===============  ====================================================
612  key                      sub-key        explanation
613======================  ===============  ====================================================
614Data                          \           A dict that contains the
615                                          reflection table,
616                                          as described in the
617                                          :ref:`Single Crystal Reflections
618                                          <XtalRefl_table>`
619                                          description.
620
621Instrument Parameters         \           A list containing two dicts where the possible
622                                          keys in each dict are listed below. The value
623                                          for most items is a list containing two values:
624                                          the initial value, the current value.
625                                          The first and second
626                                          values are floats unless otherwise noted.
627\                         Lam             Specifies a wavelength in Angstroms (two floats)
628\                         Type            Histogram type (two str values):
629                                           * 'SXC' for constant wavelength x-ray
630                                           * 'SNC' for constant wavelength neutron
631                                           * 'SNT' for time of flight neutron
632\                         InstrName       A name for the instrument, used in preparing
633                                          a CIF (str).
634
635wtFactor                      \           A weighting factor to increase or decrease
636                                          the leverage of data in the histogram (float).
637                                          A value of 1.0 weights the data with their
638                                          standard uncertainties and a larger value
639                                          increases the weighting of the data (equivalent
640                                          to decreasing the uncertainties).
641
642hId                           \           The number assigned to the histogram when
643                                          the project is loaded or edited (can change)
644ranId                         \           A random number id for the histogram
645                                          that does not change
646======================  ===============  ====================================================
647
648Single Crystal Reflection Data Structure
649----------------------------------------
650
651.. _XtalRefl_table:
652
653.. index::
654   single: Single Crystal reflection object description
655   single: Data object descriptions; Single Crystal Reflections
656   
657For every simgle crystal a histogram, the ``'Data'`` item contains
658the structure factors as an np.array in item `'RefList'`.
659The columns in that array are documented below.
660
661==========  ====================================================
662  index         explanation
663==========  ====================================================
664 0,1,2       h,k,l (float)
665 3           multiplicity
666 4           d-space, Angstrom
667 5           :math:`F_{obs}^2`
668 6           :math:`\sigma(F_{obs}^2)`
669 7           :math:`F_{calc}^2`
670 8           :math:`F_{obs}^2T`
671 9           :math:`F_{calc}^2T`
672 10          reflection phase, in degrees
673 11          intensity correction for reflection, this times
674             :math:`F_{obs}^2` or :math:`F_{calc}^2`
675             gives Iobs or Icalc
676==========  ====================================================
677
678
679*Classes and routines*
680----------------------
681
682'''
683import random as ran
684import sys
685import GSASIIpath
686import GSASIImath as G2mth
687
688GSASIIpath.SetVersionNumber("$Revision: 1147 $")
689
690DefaultControls = {
691    'deriv type':'analytic Hessian',    #default controls
692    'min dM/M':0.0001,'shift factor':1.,'max cyc':3,'F**2':True,
693    'minF/sig':0,
694    'Author':'no name',
695    'FreeVar1':'Sample humidity (%)',
696    'FreeVar2':'Sample voltage (V)',
697    'FreeVar3':'Applied load (MN)',
698    }
699'''Values to be used as defaults for the initial contents of the ``Controls``
700data tree item.
701'''
702
703def MakeUniqueLabel(lbl,labellist):
704    '''Make sure that every a label is unique against a list by adding
705    digits at the end until it is not found in list.
706
707    :param str lbl: the input label
708    :param list labellist: the labels that have already been encountered
709    :returns: lbl if not found in labellist or lbl with ``_1-9` (or
710      ``_10-99``, etc.) appended at the end
711    '''
712    lbl = lbl.strip()
713    if not lbl: # deal with a blank label
714        lbl = '_1'
715    if lbl not in labellist:
716        labellist.append(lbl)
717        return lbl
718    i = 1
719    prefix = lbl
720    if '_' in lbl:
721        prefix = lbl[:lbl.rfind('_')]
722        suffix = lbl[lbl.rfind('_')+1:]
723        try:
724            i = int(suffix)+1
725        except: # suffix could not be parsed
726            i = 1
727            prefix = lbl
728    while prefix+'_'+str(i) in labellist:
729        i += 1
730    else:
731        lbl = prefix+'_'+str(i)
732        labellist.append(lbl)
733    return lbl
734
735PhaseIdLookup = {}
736'''dict listing phase name and random Id keyed by sequential phase index as a str;
737best to access this using :func:`LookupPhaseName`
738'''
739PhaseRanIdLookup = {}
740'''dict listing phase sequential index keyed by phase random Id;
741best to access this using :func:`LookupPhaseId`
742'''
743HistIdLookup = {}
744'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
745best to access this using :func:`LookupHistName`
746'''
747HistRanIdLookup = {}
748'''dict listing histogram sequential index keyed by histogram random Id;
749best to access this using :func:`LookupHistId`
750'''
751AtomIdLookup = {}
752'''dict listing for each phase index as a str, the atom label and atom random Id,
753keyed by atom sequential index as a str;
754best to access this using :func:`LookupAtomLabel`
755'''
756AtomRanIdLookup = {}
757'''dict listing for each phase the atom sequential index keyed by atom random Id;
758best to access this using :func:`LookupAtomId`
759'''
760ShortPhaseNames = {}
761'''a dict containing a possibly shortened and when non-unique numbered
762version of the phase name. Keyed by the phase sequential index.
763'''
764ShortHistNames = {}
765'''a dict containing a possibly shortened and when non-unique numbered
766version of the histogram name. Keyed by the histogram sequential index.
767'''
768
769VarDesc = {}
770''' This dictionary lists descriptions for GSAS-II variables,
771as set in :func:`CompileVarDesc`. See that function for a description
772for how keys and values are written.
773'''
774
775reVarDesc = {}
776''' This dictionary lists descriptions for GSAS-II variables with
777the same values as :attr:`VarDesc` except that keys have been compiled as
778regular expressions. Initialized in :func:`CompileVarDesc`.
779'''
780
781def IndexAllIds(Histograms,Phases):
782    '''Scan through the used phases & histograms and create an index
783    to the random numbers of phases, histograms and atoms. While doing this,
784    confirm that assigned random numbers are unique -- just in case lightning
785    strikes twice in the same place.
786
787    Note: this code assumes that the atom random Id (ranId) is the last
788    element each atom record.
789
790    This is called in two places (only) :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
791    (which loads the histograms and phases from a GPX file) and
792    :meth:`GSASII.GSASII.GetUsedHistogramsAndPhases`
793    (which loads the histograms and phases from the data tree.)
794
795    TODO: do we need a lookup for rigid body variables?
796    '''
797    # process phases and atoms
798    PhaseIdLookup.clear()
799    PhaseRanIdLookup.clear()   
800    AtomIdLookup.clear()
801    AtomRanIdLookup.clear()
802    ShortPhaseNames.clear()
803    for ph in Phases:
804        cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
805        ranId = Phases[ph]['ranId'] 
806        while ranId in PhaseRanIdLookup:
807            # Found duplicate random Id! note and reassign
808            print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
809            Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxint)
810        pId = str(Phases[ph]['pId'])
811        PhaseIdLookup[pId] = (ph,ranId)
812        PhaseRanIdLookup[ranId] = pId
813        shortname = ph[:10]
814        while shortname in ShortPhaseNames.values():
815            shortname = ph[:8] + ' ('+ pId + ')'
816        ShortPhaseNames[pId] = shortname
817        AtomIdLookup[pId] = {}
818        AtomRanIdLookup[pId] = {}
819        for iatm,at in enumerate(Phases[ph]['Atoms']):
820            ranId = at[-1]
821            while ranId in AtomRanIdLookup[pId]: # check for dups
822                print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
823                at[-1] = ranId = ran.randint(0,sys.maxint)
824            AtomRanIdLookup[pId][ranId] = str(iatm)
825            if Phases[ph]['General']['Type'] == 'macromolecular':
826                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
827            else:
828                label = at[ct-1]
829            AtomIdLookup[pId][str(iatm)] = (label,ranId)
830    # process histograms
831    HistIdLookup.clear()
832    HistRanIdLookup.clear()
833    ShortHistNames.clear()
834    for hist in Histograms:
835        ranId = Histograms[hist]['ranId']
836        while ranId in HistRanIdLookup:
837            # Found duplicate random Id! note and reassign
838            print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
839            Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxint)
840        hId = str(Histograms[hist]['hId'])
841        HistIdLookup[hId] = (hist,ranId)
842        HistRanIdLookup[ranId] = hId
843        shortname = hist[:15]
844        while shortname in ShortHistNames.values():
845            shortname = hist[:11] + ' ('+ hId + ')'
846        ShortHistNames[hId] = shortname
847
848def LookupAtomId(pId,ranId):
849    '''Get the atom number from a phase and atom random Id
850
851    :param int/str pId: the sequential number of the phase
852    :param int ranId: the random Id assigned to an atom
853
854    :returns: the index number of the atom (str)
855    '''
856    if not AtomRanIdLookup:
857        raise Exception,'Error: LookupAtomId called before IndexAllIds was run'
858    if pId is None or pId == '':
859        raise KeyError,'Error: phase is invalid (None or blank)'
860    pId = str(pId)
861    if pId not in AtomRanIdLookup:
862        raise KeyError,'Error: LookupAtomId does not have phase '+pId
863    if ranId not in AtomRanIdLookup[pId]:
864        raise KeyError,'Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']'
865    return AtomRanIdLookup[pId][ranId]
866
867def LookupAtomLabel(pId,index):
868    '''Get the atom label from a phase and atom index number
869
870    :param int/str pId: the sequential number of the phase
871    :param int index: the index of the atom in the list of atoms
872
873    :returns: the label for the atom (str) and the random Id of the atom (int)
874    '''
875    if not AtomIdLookup:
876        raise Exception,'Error: LookupAtomLabel called before IndexAllIds was run'
877    if pId is None or pId == '':
878        raise KeyError,'Error: phase is invalid (None or blank)'
879    pId = str(pId)
880    if pId not in AtomIdLookup:
881        raise KeyError,'Error: LookupAtomLabel does not have phase '+pId
882    if index not in AtomIdLookup[pId]:
883        raise KeyError,'Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']'
884    return AtomIdLookup[pId][index]
885
886def LookupPhaseId(ranId):
887    '''Get the phase number and name from a phase random Id
888
889    :param int ranId: the random Id assigned to a phase
890    :returns: the sequential Id (pId) number for the phase (str)
891    '''
892    if not PhaseRanIdLookup:
893        raise Exception,'Error: LookupPhaseId called before IndexAllIds was run'
894    if ranId not in PhaseRanIdLookup:
895        raise KeyError,'Error: LookupPhaseId does not have ranId '+str(ranId)
896    return PhaseRanIdLookup[ranId]
897
898def LookupPhaseName(pId):
899    '''Get the phase number and name from a phase Id
900
901    :param int/str pId: the sequential assigned to a phase
902    :returns:  (phase,ranId) where phase is the name of the phase (str)
903      and ranId is the random # id for the phase (int)
904    '''
905    if not PhaseIdLookup:
906        raise Exception,'Error: LookupPhaseName called before IndexAllIds was run'
907    if pId is None or pId == '':
908        raise KeyError,'Error: phase is invalid (None or blank)'
909    pId = str(pId)
910    if pId not in PhaseIdLookup:
911        raise KeyError,'Error: LookupPhaseName does not have index '+pId
912    return PhaseIdLookup[pId]
913
914def LookupHistId(ranId):
915    '''Get the histogram number and name from a histogram random Id
916
917    :param int ranId: the random Id assigned to a histogram
918    :returns: the sequential Id (hId) number for the histogram (str)
919    '''
920    if not HistRanIdLookup:
921        raise Exception,'Error: LookupHistId called before IndexAllIds was run'
922    if ranId not in HistRanIdLookup:
923        raise KeyError,'Error: LookupHistId does not have ranId '+str(ranId)
924    return HistRanIdLookup[ranId]
925
926def LookupHistName(hId):
927    '''Get the histogram number and name from a histogram Id
928
929    :param int/str hId: the sequential assigned to a histogram
930    :returns:  (hist,ranId) where hist is the name of the histogram (str)
931      and ranId is the random # id for the histogram (int)
932    '''
933    if not HistIdLookup:
934        raise Exception,'Error: LookupHistName called before IndexAllIds was run'
935    if hId is None or hId == '':
936        raise KeyError,'Error: histogram is invalid (None or blank)'
937    hId = str(hId)
938    if hId not in HistIdLookup:
939        raise KeyError,'Error: LookupHistName does not have index '+hId
940    return HistIdLookup[hId]
941
942def fmtVarDescr(varname):
943    '''Return a string with a more complete description for a GSAS-II variable
944
945    TODO: This will not handle rigid body parameters yet
946
947    :param str name: A full G2 variable name with 2 or 3
948       colons (<p>:<h>:name[:<a>])
949       
950    :returns: a string with the description
951    '''
952   
953    l = getVarDescr(varname)
954    if not l:
955        return "invalid variable name ("+str(varname)+")!"
956
957    if not l[4]:
958        l[4] = "(variable needs a definition!)"
959
960    s = ""
961    if l[0] is not None and l[1] is not None: # HAP: keep short
962        lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
963        hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
964        if hlbl[:4] == 'HKLF':
965            hlbl = 'Xtl='+hlbl[5:]
966        elif hlbl[:4] == 'PWDR':
967            hlbl = 'Pwd='+hlbl[5:]
968        else:
969            hlbl = 'Hist='+hlbl
970        s = "Ph="+str(lbl)+" * "+str(hlbl)+": "
971    elif l[3] is not None: # atom parameter,
972        lbl = ShortPhaseNames.get(l[0],'phase?')
973        try:
974            albl = LookupAtomLabel(l[0],l[3])[0]
975        except KeyError:
976            albl = 'Atom?'
977        s = "Atom "+str(albl)+" in "+str(lbl)+": "
978    elif l[0] is not None:
979        lbl = ShortPhaseNames.get(l[0],'phase?')
980        s = "Phase "+str(lbl)+": "
981    elif l[1] is not None:
982        hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
983        if hlbl[:4] == 'HKLF':
984            hlbl = 'Xtl='+hlbl[5:]
985        elif hlbl[:4] == 'PWDR':
986            hlbl = 'Pwd='+hlbl[5:]
987        else:
988            hlbl = 'Hist='+hlbl
989        s = str(hlbl)+": "   
990    if not s:
991        s = 'Global: '
992    s += l[4]
993    return s
994
995def getVarDescr(varname):
996    '''Return a short description for a GSAS-II variable
997
998    :param str name: A full G2 variable name with 2 or 3
999       colons (<p>:<h>:name[:<a>])
1000     
1001    :returns: a five element list as [`p`,`h`,`name`,`a`,`description`],
1002      where `p`, `h`, `a` are str values or `None`, for the phase number,
1003      the histogram number and the atom number; `name` will always be
1004      an str; and `description` is str or `None`.
1005      If the variable name is incorrectly formed (for example, wrong
1006      number of colons), `None` is returned instead of a list.
1007    '''
1008    l = varname.split(':')
1009    if len(l) == 3:
1010        l += [None]
1011    if len(l) != 4:
1012        return None
1013    for i in (0,1,3):
1014        if l[i] == "":
1015            l[i] = None
1016    l += [getDescr(l[2])]
1017    return l
1018   
1019def CompileVarDesc():
1020    '''Set the values in the variable description lookup table (:attr:`VarDesc`)
1021    into :attr:`reVarDesc`. This is called in :func:`getDescr` so the initialization
1022    is always done before use.
1023
1024    Note that keys may contain regular expressions, where '[xyz]'
1025    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range of values).
1026    '.*' matches any string. For example::
1027
1028    'AUiso':'Atomic isotropic displacement parameter',
1029
1030    will match variable ``'p::AUiso:a'``.
1031    If parentheses are used in the key, the contents of those parentheses can be
1032    used in the value, such as::
1033
1034    'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1035
1036    will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
1037    in the value when used.
1038   
1039    '''
1040    import re
1041    if reVarDesc: return # already done
1042    for key,value in {
1043        # Phase vars (p::<var>)
1044        'A([0-5])' : 'Reciprocal metric tensor component \\1',
1045        'Vol' : 'Unit cell volume????',
1046        # Atom vars (p::<var>:a)
1047        'dA([xyz])' : 'change to atomic position \\1',
1048        'AUiso':'Atomic isotropic displacement parameter',
1049        'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
1050        'Afrac': 'Atomic occupancy parameter',
1051        # Hist & Phase (HAP) vars (p:h:<var>)
1052        'Bab([AU])': 'Babinet solvent scattering coef. \\1',
1053        'D([123][123])' : 'Anisotropic strain coef. \\1',
1054        'Extinction' : 'Extinction coef.',
1055        'MD' : 'March-Dollase coef.',
1056        'Mustrain;.*' : 'Microstrain coef.',
1057        'Scale' : 'Phase scale factor',
1058        'Size;.*' : 'Crystallite size value',
1059        'eA' : '?',
1060        #Histogram vars (:h:<var>)
1061        'Absorption' : 'Absorption coef.',
1062        'Displace([XY])' : 'Debye-Scherrer sample displacement \\1',
1063        'Lam' : 'Wavelength',
1064        'Polariz\.' : 'Polarization correction',
1065        'SH/L' : 'FCJ peak asymmetry correction',
1066        'Scale' : 'Histogram scale factor',
1067        '([UVW])' : 'Gaussian instrument broadening \\1',
1068        '([XY])' : 'Cauchy instrument broadening \\1',
1069        'Zero' : 'Debye-Scherrer zero correction',
1070        'nDebye' : 'Debye model background corr. terms',
1071        'nPeaks' : 'Fixed peak background corr. terms',
1072        # Global vars (::<var>)
1073        }.items():
1074        VarDesc[key] = value
1075        reVarDesc[re.compile(key)] = value
1076
1077def getDescr(name):
1078    '''Return a short description for a GSAS-II variable
1079
1080    :param str name: The descriptive part of the variable name without colons (:)
1081     
1082    :returns: a short description or None if not found
1083    '''
1084
1085    CompileVarDesc() # compile the regular expressions, if needed
1086    for key in reVarDesc:
1087        m = key.match(name)
1088        if m:
1089            return m.expand(reVarDesc[key])
1090    return None
1091
1092def _lookup(dic,key):
1093    '''Lookup a key in a dictionary, where None returns an empty string
1094    but an unmatched key returns a question mark. Used in :class:`G2VarObj`
1095    '''
1096    if key is None:
1097        return ""
1098    else:
1099        return dic.get(key,'?')
1100
1101class G2VarObj(object):
1102    '''Defines a GSAS-II variable either using the phase/atom/histogram
1103    unique Id numbers or using a character string that specifies
1104    variables by phase/atom/histogram number (which can change).
1105    Note that :func:`LoadID` should be used to (re)load the current Ids
1106    before creating or later using the G2VarObj object.
1107
1108    A :class:`G2VarObj` object can be created with a single parameter:
1109   
1110    :param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
1111      object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
1112
1113     * p is the phase number (which may be left blank);
1114     * h is the histogram number (which may be left blank);
1115     * a is the atom number (which may be left blank in which case the third colon is omitted).
1116
1117      Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
1118      Phase, Histogram, and AtomID are None or are ranId values and VarName is a string.     
1119
1120    If four positional arguments are supplied, they are:
1121
1122    :param str/int phasenum: The number for the phase
1123    :param str/int histnum: The number for the histogram
1124    :param str varname: a single value can be used to create a :class:`G2VarObj`
1125    :param str/int atomnum: The number for the atom
1126   
1127    '''
1128    IDdict = {}
1129    IDdict['phases'] = {}
1130    IDdict['hists'] = {}
1131    IDdict['atoms'] = {}
1132    def __init__(self,*args):
1133        self.phase = None
1134        self.histogram = None
1135        self.name = ''
1136        self.atom = None
1137        if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
1138            self.phase,self.histogram,self.name,self.atom = args[0]
1139        elif len(args) == 1 and ':' in args[0]:           
1140            lst = args[0].split(':')
1141            self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
1142            self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
1143            self.name = lst[2]
1144            if len(lst) > 3:
1145                self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
1146        elif len(args) == 4:
1147            self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
1148            self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
1149            self.name = args[2]
1150            self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
1151        else:
1152            raise Exception,"Incorrectly called GSAS-II parameter name"
1153
1154        #print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
1155
1156    def __str__(self):
1157        return self.varname()
1158
1159    def varname(self):
1160        '''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
1161        string (p:h:<var>:a) or (p:h:<var>)
1162
1163        :returns: the variable name as a str
1164        '''
1165        ph = _lookup(PhaseRanIdLookup,self.phase)
1166        hist = _lookup(HistRanIdLookup,self.histogram)
1167        s = (ph + ":" + hist + ":" + 
1168             str(self.name))
1169        if self.atom:
1170            if ph in AtomRanIdLookup:
1171                s += ":" + AtomRanIdLookup[ph].get(self.atom,'?')
1172            else:
1173                s += ":?"
1174        return s
1175   
1176    def __repr__(self):
1177        '''Return the detailed contents of the object
1178        '''
1179        s = "<"
1180        if self.phase is not None:
1181            ph =  _lookup(PhaseRanIdLookup,self.phase)
1182            s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
1183        if self.histogram is not None:
1184            hist = _lookup(HistRanIdLookup,self.histogram)
1185            s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
1186        if self.atom is not None:
1187            s += "Atom rId=" + str(self.atom)
1188            if ph in AtomRanIdLookup:
1189                s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
1190            else:
1191                s += " (#? -- not found!); "
1192        s += 'Variable name="' + str(self.name) + '">'
1193        return s+"("+self.varname()+")"
1194
1195    def __eq__(self, other):
1196        if type(other) is type(self):
1197            return (self.phase == other.phase and
1198                    self.histogram == other.histogram and
1199                    self.name == other.name and
1200                    self.atom == other.atom)
1201        return False
1202
1203    def _show(self):
1204        'For testing, shows the current lookup table'
1205        print 'phases', self.IDdict['phases']
1206        print 'hists', self.IDdict['hists']
1207        print 'atomDict', self.IDdict['atoms']
1208
Note: See TracBrowser for help on using the repository browser.