Source code for GSASIIobj
# -*- coding: utf-8 -*-
#GSASIIobj - data objects for GSAS-II
########### SVN repository information ###################
# $Date: 2015-07-09 17:00:23 -0500 (Thu, 09 Jul 2015) $
# $Author: vondreele $
# $Revision: 1924 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIobj.py $
# $Id: GSASIIobj.py 1924 2015-07-09 22:00:23Z vondreele $
########### SVN repository information ###################
'''
*GSASIIobj: Data objects*
=========================
This module defines and/or documents the data structures used in GSAS-II, as well
as provides misc. support routines.
Constraints Tree Item
----------------------
.. _Constraints_table:
.. index::
single: Constraints object description
single: Data object descriptions; Constraints
Constraints are stored in a dict, separated into groups.
Note that parameter are named in the following pattern,
p:h:<var>:n, where p is the phase number, h is the histogram number
<var> is a variable name and n is the parameter number.
If a parameter does not depend on a histogram or phase or is unnumbered, that
number is omitted.
Note that the contents of each dict item is a List where each element in the
list is a :ref:`constraint definition objects <Constraint_definitions_table>`.
The constraints in this form are converted in
:func:`GSASIIstrIO.ProcessConstraints` to the form used in :mod:`GSASIImapvars`
The keys in the Constraints dict are:
.. tabularcolumns:: |l|p{4.5in}|
========== ====================================================
key explanation
========== ====================================================
Hist This specifies a list of constraints on
histogram-related parameters,
which will be of form :h:<var>:n.
HAP This specifies a list of constraints on parameters
that are defined for every histogram in each phase
and are of form p:h:<var>:n.
Phase This specifies a list of constraints on phase
parameters,
which will be of form p::<var>:n.
Global This specifies a list of constraints on parameters
that are not tied to a histogram or phase and
are of form ::<var>:n
========== ====================================================
.. _Constraint_definitions_table:
.. index::
single: Constraint definition object description
single: Data object descriptions; Constraint Definition
Each constraint is defined as an item in a list. Each constraint is of form::
[[<mult1>, <var1>], [<mult2>, <var2>],..., <fixedval>, <varyflag>, <constype>]
Where the variable pair list item containing two values [<mult>, <var>], where:
* <mult> is a multiplier for the constraint (float)
* <var> a :class:`G2VarObj` object (previously a str variable name of form
'p:h:name[:at]')
Note that the last three items in the list play a special role:
* <fixedval> is the fixed value for a `constant equation` (``constype=c``)
constraint or is None. For a `New variable` (``constype=f``) constraint,
a variable name can be specified as a str (used for externally
generated constraints)
* <varyflag> is True or False for `New variable` (``constype=f``) constraints
or is None. This will be implemented in the future to indicate if these variables
should be refined.
* <constype> is one of four letters, 'e', 'c', 'h', 'f' that determines the type of constraint:
* 'e' defines a set of equivalent variables. Only the first variable is refined (if the
appropriate refine flag is set) and and all other equivalent variables in the list
are generated from that variable, using the appropriate multipliers.
* 'c' defines a constraint equation of form,
:math:`m_1 \\times var_1 + m_2 \\times var_2 + ... = c`
* 'h' defines a variable to hold (not vary). Any variable on this list is not varied,
even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
constraint and the mult value is ignored.
This is of particular value when needing to hold one or more variables where a
single flag controls a set of variables such as, coordinates,
the reciprocal metric tensor or anisotropic displacement parameter.
* 'f' defines a new variable (function) according to relationship
:math:`newvar = m_1 \\times var_1 + m_2 \\times var_2 + ...`
Covariance Tree Item
--------------------
.. _Covariance_table:
.. index::
single: Covariance description
single: Data object descriptions; Covariance
The Covariance tree item has results from the last least-squares run. They
are stored in a dict with these keys:
.. tabularcolumns:: |l|l|p{4in}|
============= =============== ====================================================
key sub-key explanation
============= =============== ====================================================
newCellDict \ dict with lattice parameters computed by
:func:`GSASIIstrMath.GetNewCellParms` (dict)
title \ Name of gpx file(?) (str)
variables \ Values for all N refined variables
(list of float values, length N,
ordered to match varyList)
sig \ Uncertainty values for all N refined variables
(list of float values, length N,
ordered to match varyList)
varyList \ List of directly refined variables
(list of str values, length N)
newAtomDict \ dict with atom position values computed in
:func:`GSASIIstrMath.ApplyXYZshifts` (dict)
Rvals \ R-factors, GOF, Marquardt value for last
refinement cycle (dict)
\ Nobs Number of observed data points (int)
\ Rwp overall weighted profile R-factor (%, float)
\ chisq sum[w*(Iobs-Icalc)**2] for all data
note this is not the reduced chi squared (float)
\ lamMax Marquardt value applied to Hessian diagonal
(float)
\ GOF The goodness-of-fit, aka square root of
the reduced chi squared. (float)
covMatrix \ The (NxN) covVariance matrix (np.array)
============= =============== ====================================================
Phase Tree Items
----------------
.. _Phase_table:
.. index::
single: Phase object description
single: Data object descriptions; Phase
Phase information is stored in the GSAS-II data tree as children of the
Phases item in a dict with keys:
.. tabularcolumns:: |l|l|p{4in}|
========== =============== ====================================================
key sub-key explanation
========== =============== ====================================================
General \ Overall information for the phase (dict)
\ AtomPtrs list of four locations to use to pull info
from the atom records (list)
\ F000X x-ray F(000) intensity (float)
\ F000N neutron F(000) intensity (float)
\ Mydir directory of current .gpx file (str)
\ MCSA controls Monte Carlo-Simulated Annealing controls (dict)
\ Cell List with 8 items: cell refinement flag (bool)
a, b, c, (Angstrom, float)
alpha, beta & gamma (degrees, float)
volume (A^3, float)
\ Type 'nuclear' or 'macromolecular' for now (str)
\ Map dict of map parameters
\ SH Texture dict of spherical harmonic preferred orientation
parameters
\ Isotope dict of isotopes for each atom type
\ Isotopes dict of scattering lengths for each isotope
combination for each element in phase
\ Name phase name (str)
\ SGData Space group details as a :ref:`space group (SGData) object <SGData_table>`
as defined in :func:`GSASIIspc.SpcGroup`.
\ Pawley neg wt Restraint value for negative Pawley intensities
(float)
\ Flip dict of Charge flip controls
\ Data plot type data plot type ('Mustrain', 'Size' or
'Preferred orientation') for powder data (str)
\ Mass Mass of unit cell contents in g/mol
\ POhkl March-Dollase preferred orientation direction
\ Z dict of atomic numbers for each atom type
\ vdWRadii dict of van der Waals radii for each atom type
\ Color Colors for atoms (list of (r,b,g) triplets)
\ AtomTypes List of atom types
\ AtomMass List of masses for atoms
\ doPawley Flag for Pawley intensity extraction (bool)
\ NoAtoms Number of atoms per unit cell of each type (dict)
\ Pawley dmin maximum Q (as d-space) to use for Pawley
extraction (float)
\ BondRadii Default radius for each atom used to compute
interatomic distances (list of floats)
\ AngleRadii Default radius for each atom used to compute
interatomic angles (list of floats)
\ DisAglCtls Dict with distance/angle search controls,
which has keys 'Name', 'AtomTypes',
'BondRadii', 'AngleRadii' which are as above
except are possibly edited. Also contains
'Factors', which is a 2 element list with
a multiplier for bond and angle search range
[typically (0.85,0.85)].
ranId \ unique random number Id for phase (int)
pId \ Phase Id number for current project (int).
Atoms \ Atoms in phase as a list of lists. The outer list
is for each atom, the inner list contains varying
items depending on the type of phase, see
the :ref:`Atom Records <Atoms_table>` description.
(list of lists)
Drawing \ Display parameters (dict)
\ ballScale Size of spheres in ball-and-stick display (float)
\ bondList dict with bonds
\ contourLevel map contour level in e/A^3 (float)
\ showABC Flag to show view point triplet (bool). True=show.
\ viewDir cartesian viewing direction (np.array with three
elements)
\ Zclip clipping distance in A (float)
\ backColor background for plot as and R,G,B triplet
(default = [0, 0, 0], black).
(list with three atoms)
\ selectedAtoms List of selected atoms (list of int values)
\ showRigidBodies Flag to highlight rigid body placement
\ sizeH Size ratio for H atoms (float)
\ bondRadius Size of binds in A (float)
\ atomPtrs positions of x, type, site sym, ADP flag in Draw Atoms (list)
\ viewPoint list of lists. First item in list is [x,y,z]
in fractional coordinates for the center of
the plot. Second item list of previous & current
atom number viewed (may be [0,0])
\ showHydrogen Flag to control plotting of H atoms.
\ unitCellBox Flag to control display of the unit cell.
\ ellipseProb Probability limit for display of thermal
ellipsoids in % (float).
\ vdwScale Multiplier of van der Waals radius for
display of vdW spheres.
\ Atoms A list of lists with an entry for each atom
that is plotted.
\ Zstep Step to de/increase Z-clip (float)
\ Quaternion Viewing quaternion (4 element np.array)
\ radiusFactor Distance ratio for searching for bonds. ? Bonds
are located that are within r(Ra+Rb) and (Ra+Rb)/r
where Ra and Rb are the atomic radii.
\ oldxy previous view point (list with two floats)
\ cameraPos Viewing position in A for plot (float)
\ depthFog True if use depthFog on plot - set currently as False (bool)
RBModels \ Rigid body assignments (note Rigid body definitions
are stored in their own main top-level tree entry.)
Pawley ref \ Pawley reflections
Histograms \ A dict of dicts. The key for the outer dict is
the histograms tied to this phase. The inner
dict contains the combined phase/histogram
parameters for items such as scale factors,
size and strain parameters. (dict)
MCSA \ Monte-Carlo simulated annealing parameters (dict)
\
========== =============== ====================================================
Rigid Body Objects
------------------
.. _RBData_table:
.. index::
single: Rigid Body Data description
single: Data object descriptions; Rigid Body Data
Rigid body descriptions are available for two types of rigid bodies: 'Vector'
and 'Residue'. Vector rigid bodies are developed by a sequence of translations each
with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
with defined refinable torsion angles.
.. tabularcolumns:: |l|l|p{4in}|
========== =============== ====================================================
key sub-key explanation
========== =============== ====================================================
Vector RBId vector rigid bodies (dict of dict)
\ AtInfo Drad, Color: atom drawing radius & color for each atom type (dict)
\ RBname Name assigned by user to rigid body (str)
\ VectMag vector magnitudes in A (list)
\ rbXYZ Cartesian coordinates for Vector rigid body (list of 3 float)
\ rbRef 3 assigned reference atom nos. in rigid body for origin
definition, use center of atoms flag (list of 3 int & 1 bool)
\ VectRef refinement flags for VectMag values (list of bool)
\ rbTypes Atom types for each atom in rigid body (list of str)
\ rbVect Cartesian vectors for each translation used to build rigid body (list of lists)
\ useCount Number of times rigid body is used in any structure (int)
Residue RBId residue rigid bodies (dict of dict)
\ AtInfo Drad, Color: atom drawing radius & color for each atom type(dict)
\ RBname Name assigned by user to rigid body (str)
\ rbXYZ Cartesian coordinates for Residue rigid body (list of 3 float)
\ rbTypes Atom types for each atom in rigid body (list of str)
\ atNames Names of each atom in rigid body (e.g. C1,N2...) (list of str)
\ rbRef 3 assigned reference atom nos. in rigid body for origin
definition, use center of atoms flag (list of 3 int & 1 bool)
\ rbSeq Orig,Piv,angle,Riding (list): definition of internal rigid body
torsion; origin atom (int), pivot atom (int), torsion angle (float),
riding atoms (list of int)
\ SelSeq [int,int] used by SeqSizer to identify objects
\ useCount Number of times rigid body is used in any structure (int)
RBIds \ unique Ids generated upon creation of each rigid body (dict)
\ Vector Ids for each Vector rigid body (list)
\ Residue Ids for each Residue rigid body (list)
========== =============== ====================================================
Space Group Objects
-------------------
.. _SGData_table:
.. index::
single: Space Group Data description
single: Data object descriptions; Space Group Data
Space groups are interpreted by :func:`GSASIIspc.SpcGroup`
and the information is placed in a SGdata object
which is a dict with these keys:
.. tabularcolumns:: |l|p{4.5in}|
========== ====================================================
key explanation
========== ====================================================
SpGrp space group symbol (str)
Laue one of the following 14 Laue classes:
-1, 2/m, mmm, 4/m, 4/mmm, 3R,
3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
SGInv True if centrosymmetric, False if not (bool)
SGLatt Lattice centering type. Will be one of
P, A, B, C, I, F, R (str)
SGUniq unique axis if monoclinic. Will be
a, b, or c for monoclinic space groups.
Will be blank for non-monoclinic. (str)
SGCen Symmetry cell centering vectors. A (n,3) np.array
of centers. Will always have at least one row:
``np.array([[0, 0, 0]])``
SGOps symmetry operations as a list of form
``[[M1,T1], [M2,T2],...]``
where :math:`M_n` is a 3x3 np.array
and :math:`T_n` is a length 3 np.array.
Atom coordinates are transformed where the
Asymmetric unit coordinates [X is (x,y,z)]
are transformed using
:math:`X^\prime = M_n*X+T_n`
SGSys symmetry unit cell: type one of
'triclinic', 'monoclinic', 'orthorhombic',
'tetragonal', 'rhombohedral', 'trigonal',
'hexagonal', 'cubic' (str)
SGPolax Axes for space group polarity. Will be one of
'', 'x', 'y', 'x y', 'z', 'x z', 'y z',
'xyz'. In the case where axes are arbitrary
'111' is used (P 1, and ?).
========== ====================================================
.. _SSGData_table:
.. index::
single: Superspace Group Data description
single: Data object descriptions; Superspace Group Data
Superspace groups [3+1] are interpreted by :func:`GSASIIspc.SSpcGroup`
and the information is placed in a SSGdata object
which is a dict with these keys:
.. tabularcolumns:: |l|p{4.5in}|
========== ====================================================
key explanation
========== ====================================================
SSpGrp superspace group symbol extension to space group
symbol, accidental spaces removed
SSGCen 4D cell centering vectors [0,0,0,0] at least
SSGOps 4D symmetry operations as [M,T] so that M*x+T = x'
========== ====================================================
Atom Records
------------
.. _Atoms_table:
.. index::
single: Atoms record description
single: Data object descriptions; Atoms record
If ``phasedict`` points to the phase information in the data tree, then
atoms are contained in a list of atom records (list) in
``phasedict['Atoms']``. Also needed to read atom information
are four pointers, ``cx,ct,cs,cia = phasedict['General']['atomPtrs']``,
which define locations in the atom record, as shown below. Items shown are
always present; additional ones for macromolecular phases are marked 'mm'
.. tabularcolumns:: |l|p{4.5in}|
============== ====================================================
location explanation
============== ====================================================
ct-4 mm - residue number (str)
ct-3 mm - residue name (e.g. ALA) (str)
ct-2 mm - chain label (str)
ct-1 atom label (str)
ct atom type (str)
ct+1 refinement flags; combination of 'F', 'X', 'U' (str)
cx,cx+1,cx+2 the x,y and z coordinates (3 floats)
cs site symmetry (str)
cs+1 site multiplicity (int)
cia ADP flag: Isotropic ('I') or Anisotropic ('A')
cia+1 Uiso (float)
cia+2...cia+7 U11, U22, U33, U12, U13, U23 (6 floats)
atom[cia+8] unique atom identifier (int)
============== ====================================================
Drawing Atom Records
--------------------
.. _Drawing_atoms_table:
.. index::
single: Drawing atoms record description
single: Data object descriptions; Drawing atoms record
If ``phasedict`` points to the phase information in the data tree, then
drawing atoms are contained in a list of drawing atom records (list) in
``phasedict['Drawing']['Atoms']``. Also needed to read atom information
are four pointers, ``cx,ct,cs,ci = phasedict['Drawing']['AtomPtrs']``,
which define locations in the atom record, as shown below. Items shown are
always present; additional ones for macromolecular phases are marked 'mm'
.. tabularcolumns:: |l|p{4.5in}|
============== ====================================================
location explanation
============== ====================================================
ct-4 mm - residue number (str)
ct-3 mm - residue name (e.g. ALA) (str)
ct-2 mm - chain label (str)
ct-1 atom label (str)
ct atom type (str)
cx,cx+1,cx+2 the x,y and z coordinates (3 floats)
cs-1 Sym Op symbol; sym. op number + unit cell id (e.g. '1,0,-1') (str)
cs atom drawing style; e.g. 'balls & sticks' (str)
cs+1 atom label style (e.g. 'name') (str)
cs+2 atom color (RBG triplet) (int)
cs+3 ADP flag: Isotropic ('I') or Anisotropic ('A')
cs+4 Uiso (float)
cs+5...cs+11 U11, U22, U33, U12, U13, U23 (6 floats)
ci unique atom identifier; matches source atom Id in Atom Records (int)
============== ====================================================
Powder Diffraction Tree Items
-----------------------------
.. _Powder_table:
.. index::
single: Powder data object description
single: Data object descriptions; Powder Data
Every powder diffraction histogram is stored in the GSAS-II data tree
with a top-level entry named beginning with the string "PWDR ". The
diffraction data for that information are directly associated with
that tree item and there are a series of children to that item. The
routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
load this information into a dictionary where the child tree name is
used as a key, and the information in the main entry is assigned
a key of ``Data``, as outlined below.
.. tabularcolumns:: |l|l|p{4in}|
====================== =============== ====================================================
key sub-key explanation
====================== =============== ====================================================
Comments \ Text strings extracted from the original powder
data header. These cannot be changed by the user;
it may be empty.
Limits \ A list of two two element lists, as [[Ld,Hd],[L,H]]
where L and Ld are the current and default lowest
two-theta value to be used and
where H and Hd are the current and default highest
two-theta value to be used.
Reflection Lists \ A dict with an entry for each phase in the
histogram. The contents of each dict item
is a dict containing reflections, as described in
the :ref:`Powder Reflections <PowderRefl_table>`
description.
Instrument Parameters \ A list containing two dicts where the possible
keys in each dict are listed below. The value
for each item is a list containing three values:
the initial value, the current value and a
refinement flag which can have a value of
True, False or 0 where 0 indicates a value that
cannot be refined. The first and second
values are floats unless otherwise noted.
Items in the first dict are noted as [1]
\ Lam Specifies a wavelength in Angstroms [1]
\ Lam1 Specifies the primary wavelength in
Angstrom, when an alpha1, alpha2
source is used [1]
\ Lam2 Specifies the secondary wavelength in
Angstrom, when an alpha1, alpha2
source is used [1]
I(L2)/I(L1) Ratio of Lam2 to Lam1 [1]
\ Type Histogram type (str) [1]:
* 'PXC' for constant wavelength x-ray
* 'PNC' for constant wavelength neutron
* 'PNT' for time of flight neutron
\ Zero Two-theta zero correction in *degrees* [1]
\ Azimuth Azimuthal setting angle for data recorded
with differing setting angles [1]
\ U, V, W Cagliotti profile coefficients
for Gaussian instrumental broadening, where the
FWHM goes as
:math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
\ X, Y Cauchy (Lorentzian) instrumental broadening
coefficients [1]
\ SH/L Variant of the Finger-Cox-Jephcoat asymmetric
peak broadening ratio. Note that this is the
average between S/L and H/L where S is
sample height, H is the slit height and
L is the goniometer diameter. [1]
\ Polariz. Polarization coefficient. [1]
wtFactor \ A weighting factor to increase or decrease
the leverage of data in the histogram (float).
A value of 1.0 weights the data with their
standard uncertainties and a larger value
increases the weighting of the data (equivalent
to decreasing the uncertainties).
Sample Parameters \ Specifies a dict with parameters that describe how
the data were collected, as listed
below. Refinable parameters are a list containing
a float and a bool, where the second value
specifies if the value is refined, otherwise
the value is a float unless otherwise noted.
\ Scale The histogram scale factor (refinable)
\ Absorption The sample absorption coefficient as
:math:`\\mu r` where r is the radius
(refinable). Only valid for Debye-Scherrer geometry.
\ SurfaceRoughA Surface roughness parameter A as defined by
Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable -
only valid for Bragg-Brentano geometry)
\ SurfaceRoughB Surface roughness parameter B (refinable -
only valid for Bragg-Brentano geometry)
\ DisplaceX, Sample displacement from goniometer center
DisplaceY where Y is along the beam direction and
X is perpendicular. Units are :math:`\\mu m`
(refinable).
\ Phi, Chi, Goniometer sample setting angles, in degrees.
Omega
\ Gonio. radius Radius of the diffractometer in mm
\ InstrName A name for the instrument, used in preparing
a CIF (str).
\ Force, Variables that describe how the measurement
Temperature, was performed. Not used directly in
Humidity, any computations.
Pressure,
Voltage
\ ranId The random-number Id for the histogram
(same value as where top-level key is ranId)
\ Type Type of diffraction data, may be 'Debye-Scherrer'
or 'Bragg-Brentano' (str).
\ Diffuse not in use?
hId \ The number assigned to the histogram when
the project is loaded or edited (can change)
ranId \ A random number id for the histogram
that does not change
Background \ The background is stored as a list with where
the first item in the list is list and the second
item is a dict. The list contains the background
function and its coefficients; the dict contains
Debye diffuse terms and background peaks.
(TODO: this needs to be expanded.)
Data \ The data consist of a list of 6 np.arrays
containing in order:
0. the x-postions (two-theta in degrees),
1. the intensity values (Yobs),
2. the weights for each Yobs value
3. the computed intensity values (Ycalc)
4. the background values
5. Yobs-Ycalc
====================== =============== ====================================================
Powder Reflection Data Structure
--------------------------------
.. _PowderRefl_table:
.. index::
single: Powder reflection object description
single: Data object descriptions; Powder Reflections
For every phase in a histogram, the ``Reflection Lists`` value is a dict
one element of which is `'RefList'`, which is a np.array containing
reflections. The columns in that array are documented below.
========== ====================================================
index explanation
========== ====================================================
0,1,2 h,k,l (float)
3 multiplicity
4 d-space, Angstrom
5 pos, two-theta
6 sig, Gaussian width
7 gam, Lorenzian width
8 :math:`F_{obs}^2`
9 :math:`F_{calc}^2`
10 reflection phase, in degrees
11 intensity correction for reflection, this times
:math:`F_{obs}^2` or :math:`F_{calc}^2` gives Iobs or Icalc
========== ====================================================
Single Crystal Tree Items
-------------------------
.. _Xtal_table:
.. index::
single: Single Crystal data object description
single: Data object descriptions; Single crystal data
Every single crystal diffraction histogram is stored in the GSAS-II data tree
with a top-level entry named beginning with the string "HKLF ". The
diffraction data for that information are directly associated with
that tree item and there are a series of children to that item. The
routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
load this information into a dictionary where the child tree name is
used as a key, and the information in the main entry is assigned
a key of ``Data``, as outlined below.
.. tabularcolumns:: |l|l|p{4in}|
====================== =============== ====================================================
key sub-key explanation
====================== =============== ====================================================
Data \ A dict that contains the
reflection table,
as described in the
:ref:`Single Crystal Reflections
<XtalRefl_table>`
description.
Instrument Parameters \ A list containing two dicts where the possible
keys in each dict are listed below. The value
for most items is a list containing two values:
the initial value, the current value.
The first and second
values are floats unless otherwise noted.
\ Lam Specifies a wavelength in Angstroms (two floats)
\ Type Histogram type (two str values):
* 'SXC' for constant wavelength x-ray
* 'SNC' for constant wavelength neutron
* 'SNT' for time of flight neutron
\ InstrName A name for the instrument, used in preparing
a CIF (str).
wtFactor \ A weighting factor to increase or decrease
the leverage of data in the histogram (float).
A value of 1.0 weights the data with their
standard uncertainties and a larger value
increases the weighting of the data (equivalent
to decreasing the uncertainties).
hId \ The number assigned to the histogram when
the project is loaded or edited (can change)
ranId \ A random number id for the histogram
that does not change
====================== =============== ====================================================
Single Crystal Reflection Data Structure
----------------------------------------
.. _XtalRefl_table:
.. index::
single: Single Crystal reflection object description
single: Data object descriptions; Single Crystal Reflections
For every single crystal a histogram, the ``'Data'`` item contains
the structure factors as an np.array in item `'RefList'`.
The columns in that array are documented below.
========== ====================================================
index explanation
========== ====================================================
0,1,2 h,k,l (float)
3 multiplicity
4 d-space, Angstrom
5 :math:`F_{obs}^2`
6 :math:`\sigma(F_{obs}^2)`
7 :math:`F_{calc}^2`
8 :math:`F_{obs}^2T`
9 :math:`F_{calc}^2T`
10 reflection phase, in degrees
11 intensity correction for reflection, this times
:math:`F_{obs}^2` or :math:`F_{calc}^2`
gives Iobs or Icalc
========== ====================================================
Image Data Structure
--------------------
.. _Image_table:
.. index::
image: Image data object description
image: Image object descriptions
Every 2-dimensional image is stored in the GSAS-II data tree
with a top-level entry named beginning with the string "IMG ". The
image data are directly associated with that tree item and there
are a series of children to that item. The routines :func:`GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
and :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` will
load this information into a dictionary where the child tree name is
used as a key, and the information in the main entry is assigned
a key of ``Data``, as outlined below.
.. tabularcolumns:: |l|l|p{4in}|
====================== ====================== ====================================================
key sub-key explanation
====================== ====================== ====================================================
Comments \ Text strings extracted from the original image data
header or a metafile. These cannot be changed by
the user; it may be empty.
Image Controls azmthOff (float) The offset to be applied to an azimuthal
value. Accomodates
detector orientations other than with the detector
X-axis
horizontal.
\ background image (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
during image integration multiplied by value. It must have the same size/shape as
the integrated image. NB: value < 0 for subtraction.
\ calibrant (str) The material used for determining the position/orientation
of the image. The data is obtained from :func:`ImageCalibrants`
and UserCalibrants.py (supplied by user).
\ calibdmin (float) The minimum d-spacing used during the last calibration run.
\ calibskip (int) The number of expected diffraction lines skipped during the last
calibration run.
\ center (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
strikes the detector plane as determined by calibration. This point
does not have to be within the limits of the detector boundaries.
\ centerAzm (bool) If True then the azimuth reported for the integrated slice
of the image is at the center line otherwise it is at the leading edge.
\ color (str) The name of the colormap used to display the image. Default = 'Paired'.
\ cutoff (float) The minimum value of I/Ib for a point selected in a diffraction ring for
calibration calculations. See pixLimit for details as how point is found.
\ DetDepth (float) Coefficient for penetration correction to distance; accounts for diffraction
ring offset at higher angles. Optionally determined by calibration.
\ DetDepthRef (bool) If True then refine DetDepth during calibration/recalibration calculation.
\ distance (float) The distance (mm) from sample to detector plane.
\ ellipses (list:lists) Each object in ellipses is a list [center,phi,radii,color] where
center (list) is location (mm) of the ellipse center on the detector plane, phi is the
rotation of the ellipse minor axis from the x-axis, and radii are the minor & major
radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola.
\ edgemin (float) Not used; parameter in EdgeFinder code.
\ fullIntegrate (bool) If True then integrate over full 360 deg azimuthal range.
\ GonioAngles (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.
Required for texture calculations.
\ invert_x (bool) If True display the image with the x-axis inverted.
\ invert_y (bool) If True display the image with the y-axis inverted.
\ IOtth (list:floats) The minimum and maximum 2-theta values to be used for integration.
\ LRazimuth (list:floats) The minimum and maximum azimuth values to be used for integration.
\ Oblique (list:float,bool) If True apply a detector absorption correction using the value to the
intensities obtained during integration.
\ outAzimuths (int) The number of azimuth pie slices.
\ outChannels (int) The number of 2-theta steps.
\ pixelSize (list:ints) The X,Y dimensions (microns) of each pixel.
\ pixLimit (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax`
and subject to cutoff in :func:`GSASIIimage.makeRing`.
Locations are used to construct rings of points for calibration calcualtions.
\ PolaVal (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from
integration using value.
\ rings (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a
diffraction ring with the same d-spacing (dsp)
\ ring (list) The x,y coordinates of the >5 points on an inner ring
selected by the user,
\ Range (list) The minimum & maximum values of the image
\ rotation (float) The angle between the x-axis and the vector about which the
detector is tilted. Constrained to -180 to 180 deg.
\ SampleShape (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption
calculations.
\ SampleAbs (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
to cause correction to be applied.
\ setDefault (bool) If True the use the image controls values for all new images to be read. (might be removed)
\ setRings (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.
\ showLines (bool) If True then isplay the integration limits to be used.
\ size (list:int) The number of pixels on the image x & y axes
\ type (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.
\ tilt (float) The angle the detector normal makes with the incident beam; range -90 to 90.
\ wavelength (float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).
Masks Arcs (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
to be excluded from integration
\ Frames (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
of which is excluded from recalibration and integration. Only one frame is allowed.
\ Points (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
from integration.
\ Polygons (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
to be excluded from integration.
\ Rings (list: lists) Each entry [2-theta,thickness] describes a ring mask
to be excluded from integration.
\ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
in integrsation. The tuple is the image intensity limits and the list are those set by the user.
Stress/Strain Sample phi (float) Sample rotation about vertical axis.
\ Sample z (float) Sample translation from the calibration sample position (for Sample phi = 0)
These will be restricted by space group symmetry; result of strain fit refinement.
\ Type (str) 'True' or 'Conventional': The strain model used for the calculation.
\ 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.
The dictionary items are:
'Dset': (float) True d-spacing for the diffraction ring; entered by the user.
'Dcalc': (float) Average calculated d-spacing determined from strain coeff.
'Emat': (list: float) The strain tensor elements e11, e12 & e22 (e21=e12, rest are 0)
'Esig': (list: float) Esds for Emat from fitting.
'pixLimit': (int) Search range to find highest point on ring for each data point
'cutoff': (float) I/Ib cutoff for searching.
'ImxyObs': (list: lists) [[X],[Y]] observed points to be used for strain calculations.
'ImtaObs': (list: lists) [[d],[azm]] transformed via detector calibration from ImxyObs.
'ImtaCalc': (list: lists [[d],[azm]] calculated d-spacing & azimuth from fit.
====================== ====================== ====================================================
Parameter Dictionary
-------------------------
.. _parmDict_table:
.. index::
single: Parameter dictionary
The parameter dictionary contains all of the variable parameters for the refinement.
The dictionary keys are the name of the parameter (<phase>:<hist>:<name>:<atom>).
It is prepared in two ways. When loaded from the tree
(in :meth:`GSASII.GSASII.MakeLSParmDict` and
:meth:`GSASIIIO.ExportBaseclass.loadParmDict`),
the values are lists with two elements: ``[value, refine flag]``
When loaded from the GPX file (in
:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`), the value in the
dict is the actual parameter value (usually a float, but sometimes a
letter or string flag value (such as I or A for iso/anisotropic).
*Classes and routines*
----------------------
'''
import re
import imp
import random as ran
import sys
import GSASIIpath
import GSASIImath as G2mth
import numpy as np
GSASIIpath.SetVersionNumber("$Revision: 1924 $")
DefaultControls = {
'deriv type':'analytic Hessian',
'min dM/M':0.0001,'shift factor':1.,'max cyc':3,'F**2':False,
'UsrReject':{'minF/sig':0,'MinExt':0.01,'MaxDF/F':100.,'MaxD':500.,'MinD':0.05},
'Copy2Next':False,'Reverse Seq':False,'HatomFix':False,
'Author':'no name',
'FreePrm1':'Sample humidity (%)',
'FreePrm2':'Sample voltage (V)',
'FreePrm3':'Applied load (MN)',
'SeqPseudoVars':{},'SeqParFitEqList':[],'ShowCell':False,
}
'''Values to be used as defaults for the initial contents of the ``Controls``
data tree item.
'''
[docs]def MakeUniqueLabel(lbl,labellist):
'''Make sure that every a label is unique against a list by adding
digits at the end until it is not found in list.
:param str lbl: the input label
:param list labellist: the labels that have already been encountered
:returns: lbl if not found in labellist or lbl with ``_1-9`` (or
``_10-99``, etc.) appended at the end
'''
lbl = lbl.strip()
if not lbl: # deal with a blank label
lbl = '_1'
if lbl not in labellist:
labellist.append(lbl)
return lbl
i = 1
prefix = lbl
if '_' in lbl:
prefix = lbl[:lbl.rfind('_')]
suffix = lbl[lbl.rfind('_')+1:]
try:
i = int(suffix)+1
except: # suffix could not be parsed
i = 1
prefix = lbl
while prefix+'_'+str(i) in labellist:
i += 1
else:
lbl = prefix+'_'+str(i)
labellist.append(lbl)
return lbl
PhaseIdLookup = {}
'''dict listing phase name and random Id keyed by sequential phase index as a str;
best to access this using :func:`LookupPhaseName`
'''
PhaseRanIdLookup = {}
'''dict listing phase sequential index keyed by phase random Id;
best to access this using :func:`LookupPhaseId`
'''
HistIdLookup = {}
'''dict listing histogram name and random Id, keyed by sequential histogram index as a str;
best to access this using :func:`LookupHistName`
'''
HistRanIdLookup = {}
'''dict listing histogram sequential index keyed by histogram random Id;
best to access this using :func:`LookupHistId`
'''
AtomIdLookup = {}
'''dict listing for each phase index as a str, the atom label and atom random Id,
keyed by atom sequential index as a str;
best to access this using :func:`LookupAtomLabel`
'''
AtomRanIdLookup = {}
'''dict listing for each phase the atom sequential index keyed by atom random Id;
best to access this using :func:`LookupAtomId`
'''
ShortPhaseNames = {}
'''a dict containing a possibly shortened and when non-unique numbered
version of the phase name. Keyed by the phase sequential index.
'''
ShortHistNames = {}
'''a dict containing a possibly shortened and when non-unique numbered
version of the histogram name. Keyed by the histogram sequential index.
'''
VarDesc = {}
''' This dictionary lists descriptions for GSAS-II variables,
as set in :func:`CompileVarDesc`. See that function for a description
for how keys and values are written.
'''
reVarDesc = {}
''' This dictionary lists descriptions for GSAS-II variables with
the same values as :attr:`VarDesc` except that keys have been compiled as
regular expressions. Initialized in :func:`CompileVarDesc`.
'''
[docs]def IndexAllIds(Histograms,Phases):
'''Scan through the used phases & histograms and create an index
to the random numbers of phases, histograms and atoms. While doing this,
confirm that assigned random numbers are unique -- just in case lightning
strikes twice in the same place.
Note: this code assumes that the atom random Id (ranId) is the last
element each atom record.
This is called in three places (only): :func:`GSASIIstrIO.GetUsedHistogramsAndPhases`
(which loads the histograms and phases from a GPX file),
:meth:`~GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree`
(which loads the histograms and phases from the data tree.) and
:meth:`GSASIIconstrGUI.UpdateConstraints`
(which displays & edits the constraints in a GUI)
TODO: do we need a lookup for rigid body variables?
'''
# process phases and atoms
PhaseIdLookup.clear()
PhaseRanIdLookup.clear()
AtomIdLookup.clear()
AtomRanIdLookup.clear()
ShortPhaseNames.clear()
for ph in Phases:
cx,ct,cs,cia = Phases[ph]['General']['AtomPtrs']
ranId = Phases[ph]['ranId']
while ranId in PhaseRanIdLookup:
# Found duplicate random Id! note and reassign
print ("\n\n*** Phase "+str(ph)+" has repeated ranId. Fixing.\n")
Phases[ph]['ranId'] = ranId = ran.randint(0,sys.maxint)
pId = str(Phases[ph]['pId'])
PhaseIdLookup[pId] = (ph,ranId)
PhaseRanIdLookup[ranId] = pId
shortname = ph #[:10]
while shortname in ShortPhaseNames.values():
shortname = ph[:8] + ' ('+ pId + ')'
ShortPhaseNames[pId] = shortname
AtomIdLookup[pId] = {}
AtomRanIdLookup[pId] = {}
for iatm,at in enumerate(Phases[ph]['Atoms']):
ranId = at[cia+8]
while ranId in AtomRanIdLookup[pId]: # check for dups
print ("\n\n*** Phase "+str(ph)+" atom "+str(iatm)+" has repeated ranId. Fixing.\n")
at[cia+8] = ranId = ran.randint(0,sys.maxint)
AtomRanIdLookup[pId][ranId] = str(iatm)
if Phases[ph]['General']['Type'] == 'macromolecular':
label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
else:
label = at[ct-1]
AtomIdLookup[pId][str(iatm)] = (label,ranId)
# process histograms
HistIdLookup.clear()
HistRanIdLookup.clear()
ShortHistNames.clear()
for hist in Histograms:
ranId = Histograms[hist]['ranId']
while ranId in HistRanIdLookup:
# Found duplicate random Id! note and reassign
print ("\n\n*** Histogram "+str(hist)+" has repeated ranId. Fixing.\n")
Histograms[hist]['ranId'] = ranId = ran.randint(0,sys.maxint)
hId = str(Histograms[hist]['hId'])
HistIdLookup[hId] = (hist,ranId)
HistRanIdLookup[ranId] = hId
shortname = hist[:15]
while shortname in ShortHistNames.values():
shortname = hist[:11] + ' ('+ hId + ')'
ShortHistNames[hId] = shortname
[docs]def LookupAtomId(pId,ranId):
'''Get the atom number from a phase and atom random Id
:param int/str pId: the sequential number of the phase
:param int ranId: the random Id assigned to an atom
:returns: the index number of the atom (str)
'''
if not AtomRanIdLookup:
raise Exception,'Error: LookupAtomId called before IndexAllIds was run'
if pId is None or pId == '':
raise KeyError,'Error: phase is invalid (None or blank)'
pId = str(pId)
if pId not in AtomRanIdLookup:
raise KeyError,'Error: LookupAtomId does not have phase '+pId
if ranId not in AtomRanIdLookup[pId]:
raise KeyError,'Error: LookupAtomId, ranId '+str(ranId)+' not in AtomRanIdLookup['+pId+']'
return AtomRanIdLookup[pId][ranId]
[docs]def LookupAtomLabel(pId,index):
'''Get the atom label from a phase and atom index number
:param int/str pId: the sequential number of the phase
:param int index: the index of the atom in the list of atoms
:returns: the label for the atom (str) and the random Id of the atom (int)
'''
if not AtomIdLookup:
raise Exception,'Error: LookupAtomLabel called before IndexAllIds was run'
if pId is None or pId == '':
raise KeyError,'Error: phase is invalid (None or blank)'
pId = str(pId)
if pId not in AtomIdLookup:
raise KeyError,'Error: LookupAtomLabel does not have phase '+pId
if index not in AtomIdLookup[pId]:
raise KeyError,'Error: LookupAtomLabel, ranId '+str(index)+' not in AtomRanIdLookup['+pId+']'
return AtomIdLookup[pId][index]
[docs]def LookupPhaseId(ranId):
'''Get the phase number and name from a phase random Id
:param int ranId: the random Id assigned to a phase
:returns: the sequential Id (pId) number for the phase (str)
'''
if not PhaseRanIdLookup:
raise Exception,'Error: LookupPhaseId called before IndexAllIds was run'
if ranId not in PhaseRanIdLookup:
raise KeyError,'Error: LookupPhaseId does not have ranId '+str(ranId)
return PhaseRanIdLookup[ranId]
[docs]def LookupPhaseName(pId):
'''Get the phase number and name from a phase Id
:param int/str pId: the sequential assigned to a phase
:returns: (phase,ranId) where phase is the name of the phase (str)
and ranId is the random # id for the phase (int)
'''
if not PhaseIdLookup:
raise Exception,'Error: LookupPhaseName called before IndexAllIds was run'
if pId is None or pId == '':
raise KeyError,'Error: phase is invalid (None or blank)'
pId = str(pId)
if pId not in PhaseIdLookup:
raise KeyError,'Error: LookupPhaseName does not have index '+pId
return PhaseIdLookup[pId]
[docs]def LookupHistId(ranId):
'''Get the histogram number and name from a histogram random Id
:param int ranId: the random Id assigned to a histogram
:returns: the sequential Id (hId) number for the histogram (str)
'''
if not HistRanIdLookup:
raise Exception,'Error: LookupHistId called before IndexAllIds was run'
if ranId not in HistRanIdLookup:
raise KeyError,'Error: LookupHistId does not have ranId '+str(ranId)
return HistRanIdLookup[ranId]
[docs]def LookupHistName(hId):
'''Get the histogram number and name from a histogram Id
:param int/str hId: the sequential assigned to a histogram
:returns: (hist,ranId) where hist is the name of the histogram (str)
and ranId is the random # id for the histogram (int)
'''
if not HistIdLookup:
raise Exception,'Error: LookupHistName called before IndexAllIds was run'
if hId is None or hId == '':
raise KeyError,'Error: histogram is invalid (None or blank)'
hId = str(hId)
if hId not in HistIdLookup:
raise KeyError,'Error: LookupHistName does not have index '+hId
return HistIdLookup[hId]
[docs]def fmtVarDescr(varname):
'''Return a string with a more complete description for a GSAS-II variable
:param str varname: A full G2 variable name with 2 or 3 or 4
colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
:returns: a string with the description
'''
s,l = VarDescr(varname)
return s+": "+l
[docs]def VarDescr(varname):
'''Return two strings with a more complete description for a GSAS-II variable
:param str name: A full G2 variable name with 2 or 3 or 4
colons (<p>:<h>:name[:<a>] or <p>::RBname:<r>:<t>])
:returns: (loc,meaning) where loc describes what item the variable is mapped
(phase, histogram, etc.) and meaning describes what the variable does.
'''
# special handling for parameter names without a colons
# for now, assume self-defining
if varname.find(':') == -1:
return "Global",varname
l = getVarDescr(varname)
if not l:
return ("invalid variable name ("+str(varname)+")!"),""
# return "invalid variable name!",""
if not l[-1]:
l[-1] = "(variable needs a definition! Set it in CompileVarDesc)"
if len(l) == 3: #SASD variable name!
s = 'component:'+l[1]
return s,l[-1]
s = ""
if l[0] is not None and l[1] is not None: # HAP: keep short
if l[2] == "Scale": # fix up ambigous name
l[5] = "Phase fraction"
if l[0] == '*':
lbl = 'Seq. ref.'
else:
lbl = ShortPhaseNames.get(l[0],'? #'+str(l[0]))
if l[1] == '*':
hlbl = 'Seq. ref.'
else:
hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
if hlbl[:4] == 'HKLF':
hlbl = 'Xtl='+hlbl[5:]
elif hlbl[:4] == 'PWDR':
hlbl = 'Pwd='+hlbl[5:]
else:
hlbl = 'Hist='+hlbl
s = "Ph="+str(lbl)+" * "+str(hlbl)
else:
if l[2] == "Scale": # fix up ambigous name: must be scale factor, since not HAP
l[5] = "Scale factor"
if l[2] == 'Back': # background parameters are "special", alas
s = 'Hist='+ShortHistNames.get(l[1],'? #'+str(l[1]))
l[-1] += ' #'+str(l[3])
elif l[4] is not None: # rigid body parameter
lbl = ShortPhaseNames.get(l[0],'phase?')
s = "Res #"+str(l[3])+" body #"+str(l[4])+" in "+str(lbl)
elif l[3] is not None: # atom parameter,
lbl = ShortPhaseNames.get(l[0],'phase?')
try:
albl = LookupAtomLabel(l[0],l[3])[0]
except KeyError:
albl = 'Atom?'
s = "Atom "+str(albl)+" in "+str(lbl)
elif l[0] == '*':
s = "All phases "
elif l[0] is not None:
lbl = ShortPhaseNames.get(l[0],'phase?')
s = "Phase "+str(lbl)
elif l[1] == '*':
s = 'All hists'
elif l[1] is not None:
hlbl = ShortHistNames.get(l[1],'? #'+str(l[1]))
if hlbl[:4] == 'HKLF':
hlbl = 'Xtl='+hlbl[5:]
elif hlbl[:4] == 'PWDR':
hlbl = 'Pwd='+hlbl[5:]
else:
hlbl = 'Hist='+hlbl
s = str(hlbl)
if not s:
s = 'Global'
return s,l[-1]
[docs]def getVarDescr(varname):
'''Return a short description for a GSAS-II variable
:param str name: A full G2 variable name with 2 or 3 or 4
colons (<p>:<h>:name[:<a1>][:<a2>])
:returns: a six element list as [`p`,`h`,`name`,`a1`,`a2`,`description`],
where `p`, `h`, `a1`, `a2` are str values or `None`, for the phase number,
the histogram number and the atom number; `name` will always be
a str; and `description` is str or `None`.
If the variable name is incorrectly formed (for example, wrong
number of colons), `None` is returned instead of a list.
'''
l = varname.split(':')
if len(l) == 2: #SASD parameter name
return varname,l[0],getDescr(l[1])
if len(l) == 3:
l += [None,None]
elif len(l) == 4:
l += [None]
elif len(l) != 5:
return None
for i in (0,1,3,4):
if l[i] == "":
l[i] = None
l += [getDescr(l[2])]
return l
[docs]def CompileVarDesc():
'''Set the values in the variable description lookup table (:attr:`VarDesc`)
into :attr:`reVarDesc`. This is called in :func:`getDescr` so the initialization
is always done before use.
Note that keys may contain regular expressions, where '[xyz]'
matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range of values).
'.*' matches any string. For example::
'AUiso':'Atomic isotropic displacement parameter',
will match variable ``'p::AUiso:a'``.
If parentheses are used in the key, the contents of those parentheses can be
used in the value, such as::
'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
will match ``AU11``, ``AU23``,.. and `U11`, `U23` etc will be displayed
in the value when used.
'''
if reVarDesc: return # already done
for key,value in {
# derived or other sequential vars
'([abc])$' : 'Lattice parameter, \\1, from Ai and Djk', # N.B. '$' prevents match if any characters follow
u'\u03B1' : u'Lattice parameter, \u03B1, from Ai and Djk',
u'\u03B2' : u'Lattice parameter, \u03B2, from Ai and Djk',
u'\u03B3' : u'Lattice parameter, \u03B3, from Ai and Djk',
# ambiguous, alas:
'Scale' : 'Phase or Histogram scale factor',
# Phase vars (p::<var>)
'A([0-5])' : 'Reciprocal metric tensor component \\1',
'Vol' : 'Unit cell volume',
# Atom vars (p::<var>:a)
'dA([xyz])$' : 'change to atomic coordinate, \\1',
'A([xyz])$' : '\\1 fractional atomic coordinate',
'AUiso':'Atomic isotropic displacement parameter',
'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
'Afrac': 'Atomic occupancy parameter',
# Hist & Phase (HAP) vars (p:h:<var>)
'Back': 'Background term',
'BkPkint;(.*)':'Background peak #\\1 intensity',
'BkPkpos;(.*)':'Background peak #\\1 position',
'BkPksig;(.*)':'Background peak #\\1 Gaussian width',
'BkPkgam;(.*)':'Background peak #\\1 Cauchy width',
'Bab([AU])': 'Babinet solvent scattering coef. \\1',
'D([123][123])' : 'Anisotropic strain coef. \\1',
'Extinction' : 'Extinction coef.',
'MD' : 'March-Dollase coef.',
'Mustrain;.*' : 'Microstrain coef.',
'Size;.*' : 'Crystallite size value',
'eA$' : 'Cubic mustrain value',
'Ep$' : 'Primary extinction',
'Es$' : 'Secondary type II extinction',
'Eg$' : 'Secondary type I extinction',
'Flack' : 'Flack parameter',
'TwinFr' : 'Twin fraction',
#Histogram vars (:h:<var>)
'Absorption' : 'Absorption coef.',
'Displace([XY])' : 'Debye-Scherrer sample displacement \\1',
'Lam' : 'Wavelength',
'Polariz\.' : 'Polarization correction',
'SH/L' : 'FCJ peak asymmetry correction',
'([UVW])$' : 'Gaussian instrument broadening \\1',
'([XY])$' : 'Cauchy instrument broadening \\1',
'Zero' : 'Debye-Scherrer zero correction',
'nDebye' : 'Debye model background corr. terms',
'nPeaks' : 'Fixed peak background corr. terms',
'RBV.*' : 'Vector rigid body parameter',
'RBR.*' : 'Residue rigid body parameter',
'RBRO([aijk])' : 'Residue rigid body orientation parameter',
'RBRP([xyz])' : 'Residue rigid body position parameter',
'RBRTr;.*' : 'Residue rigid body torsion parameter',
'RBR([TLS])([123AB][123AB])' : 'Residue rigid body group disp. param.',
'constr([0-9]*)' : 'Parameter from constraint',
# supersymmetry parameters p::<var>:a:o 'Flen','Fcent'?
'mV([0-2])$' : 'Modulation vector component \\1',
'Fsin' : 'Sin site fraction modulation',
'Fcos' : 'Cos site fraction modulation',
'Fzero' : 'Crenel function offset',
'Fwid' : 'Crenel function width',
'Tzero' : 'Sawtooth/ZigZag location',
'([XYZ])slope': 'Sawtooth/ZigZag slope for \\1',
'([XYZ])sin' : 'Sin position wave for \\1',
'([XYZ])cos' : 'Cos position wave for \\1',
'U([123][123])sin$' : 'Sin thermal wave for U\\1',
'U([123][123])cos$' : 'Cos thermal wave for U\\1',
'M([XYZ])sin$' : 'Sin mag. moment wave for \\1',
'M([XYZ])cos$' : 'Cos mag. moment wave for \\1',
# SASD vars (l:<var>;l = component)
'Aspect ratio' : 'Particle aspect ratio',
'Length' : 'Cylinder length',
'Diameter' : 'Cylinder/disk diameter',
'Thickness' : 'Disk thickness',
'Dist' : 'Interparticle distance',
'VolFr' : 'Dense scatterer volume fraction',
'epis' : 'Sticky sphere epsilon',
'Sticky' : 'Stickyness',
'Depth' : 'Well depth',
'Width' : 'Well width',
'Volume' : 'Particle volume',
'Radius' : 'Sphere/cylinder/disk radius',
'Mean' : 'Particle mean radius',
'StdDev' : 'Standard deviation in Mean',
'G$': 'Guinier prefactor',
'Rg$': 'Guinier radius of gyration',
'B$': 'Porod prefactor',
'P$': 'Porod power',
'Cutoff': 'Porod cutoff',
'PkInt': 'Bragg peak intensity',
'PkPos': 'Bragg peak position',
'PkSig': 'Bragg peak sigma',
'PkGam': 'Bragg peak gamma',
'e([12][12])' : 'strain tensor e\1', # strain vars e11, e22, e12
'Dcalc': 'Calc. d-spacing',
'Back$': 'background parameter',
'pos$': 'peak position',
'int$': 'peak intensity',
}.items():
VarDesc[key] = value
reVarDesc[re.compile(key)] = value
[docs]def getDescr(name):
'''Return a short description for a GSAS-II variable
:param str name: The descriptive part of the variable name without colons (:)
:returns: a short description or None if not found
'''
CompileVarDesc() # compile the regular expressions, if needed
for key in reVarDesc:
m = key.match(name)
if m:
reVarDesc[key]
return m.expand(reVarDesc[key])
return None
[docs]def GenWildCard(varlist):
'''Generate wildcard versions of G2 variables. These introduce '*'
for a phase, histogram or atom number (but only for one of these
fields) but only when there is more than one matching variable in the
input variable list. So if the input is this::
varlist = ['0::AUiso:0', '0::AUiso:1', '1::AUiso:0']
then the output will be this::
wildList = ['*::AUiso:0', '0::AUiso:*']
:param list varlist: an input list of GSAS-II variable names
(such as 0::AUiso:0)
:returns: wildList, the generated list of wild card variable names.
'''
wild = []
for i in (0,1,3):
currentL = varlist[:]
while currentL:
item1 = currentL.pop(0)
i1splt = item1.split(':')
if i >= len(i1splt): continue
if i1splt[i]:
nextL = []
i1splt[i] = '[0-9]+'
rexp = re.compile(':'.join(i1splt))
matchlist = [item1]
for nxtitem in currentL:
if rexp.match(nxtitem):
matchlist += [nxtitem]
else:
nextL.append(nxtitem)
if len(matchlist) > 1:
i1splt[i] = '*'
wild.append(':'.join(i1splt))
currentL = nextL
return wild
[docs]def LookupWildCard(varname,varlist):
'''returns a list of variable names from list varname
that match wildcard name in varname
:param str varname: a G2 variable name containing a wildcard
(such as \*::var)
:param list varlist: the list of all variable names used in
the current project
:returns: a list of matching GSAS-II variables (may be empty)
'''
rexp = re.compile(varname.replace('*','[0-9]+'))
return sorted([var for var in varlist if rexp.match(var)])
def _lookup(dic,key):
'''Lookup a key in a dictionary, where None returns an empty string
but an unmatched key returns a question mark. Used in :class:`G2VarObj`
'''
if key is None:
return ""
elif key == "*":
return "*"
else:
return dic.get(key,'?')
[docs]class G2VarObj(object):
'''Defines a GSAS-II variable either using the phase/atom/histogram
unique Id numbers or using a character string that specifies
variables by phase/atom/histogram number (which can change).
Note that :func:`LoadID` should be used to (re)load the current Ids
before creating or later using the G2VarObj object.
This can store rigid body variables, but does not translate the residue # and
body # to/from random Ids
A :class:`G2VarObj` object can be created with a single parameter:
:param str/tuple varname: a single value can be used to create a :class:`G2VarObj`
object. If a string, it must be of form "p:h:var" or "p:h:var:a", where
* p is the phase number (which may be left blank or may be '*' to indicate all phases);
* h is the histogram number (which may be left blank or may be '*' to indicate all histograms);
* a is the atom number (which may be left blank in which case the third colon is omitted).
The atom number can be specified as '*' if a phase number is specified (not as '*').
For rigid body variables, specify a will be a string of form "residue:body#"
Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
Phase, Histogram, and AtomID are None or are ranId values (or one can be '*')
and VarName is a string. Note that if Phase is '*' then the AtomID is an atom number.
For a rigid body variables, AtomID is a string of form "residue:body#".
If four positional arguments are supplied, they are:
:param str/int phasenum: The number for the phase (or None or '*')
:param str/int histnum: The number for the histogram (or None or '*')
:param str varname: a single value can be used to create a :class:`G2VarObj`
:param str/int atomnum: The number for the atom (or None or '*')
'''
IDdict = {}
IDdict['phases'] = {}
IDdict['hists'] = {}
IDdict['atoms'] = {}
def __init__(self,*args):
self.phase = None
self.histogram = None
self.name = ''
self.atom = None
if len(args) == 1 and (type(args[0]) is list or type(args[0]) is tuple) and len(args[0]) == 4:
# single arg with 4 values
self.phase,self.histogram,self.name,self.atom = args[0]
elif len(args) == 1 and ':' in args[0]:
#parse a string
lst = args[0].split(':')
if lst[0] == '*':
self.phase = '*'
if len(lst) > 3:
self.atom = lst[3]
self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
elif lst[1] == '*':
self.histogram = '*'
self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
else:
self.histogram = HistIdLookup.get(lst[1],[None,None])[1]
self.phase = PhaseIdLookup.get(lst[0],[None,None])[1]
if len(lst) == 4:
if lst[3] == '*':
self.atom = '*'
else:
self.atom = AtomIdLookup[lst[0]].get(lst[3],[None,None])[1]
elif len(lst) == 5:
self.atom = lst[3]+":"+lst[4]
elif len(lst) == 3:
pass
else:
raise Exception,"Too many colons in var name "+str(args[0])
self.name = lst[2]
elif len(args) == 4:
if args[0] == '*':
self.phase = '*'
self.atom = args[3]
else:
self.phase = PhaseIdLookup.get(str(args[0]),[None,None])[1]
if args[3] == '*':
self.atom = '*'
elif args[0] is not None:
self.atom = AtomIdLookup[args[0]].get(str(args[3]),[None,None])[1]
if args[1] == '*':
self.histogram = '*'
else:
self.histogram = HistIdLookup.get(str(args[1]),[None,None])[1]
self.name = args[2]
else:
raise Exception,"Incorrectly called GSAS-II parameter name"
#print "DEBUG: created ",self.phase,self.histogram,self.name,self.atom
def __str__(self):
return self.varname()
[docs] def varname(self):
'''Formats the GSAS-II variable name as a "traditional" GSAS-II variable
string (p:h:<var>:a) or (p:h:<var>)
:returns: the variable name as a str
'''
a = ""
if self.phase == "*":
ph = "*"
if self.atom:
a = ":" + str(self.atom)
else:
ph = _lookup(PhaseRanIdLookup,self.phase)
if self.atom == '*':
a = ':*'
elif self.atom:
if ":" in str(self.atom):
a = ":" + str(self.atom)
elif ph in AtomRanIdLookup:
a = ":" + AtomRanIdLookup[ph].get(self.atom,'?')
else:
a = ":?"
if self.histogram == "*":
hist = "*"
else:
hist = _lookup(HistRanIdLookup,self.histogram)
s = (ph + ":" + hist + ":" + str(self.name)) + a
return s
def __repr__(self):
'''Return the detailed contents of the object
'''
s = "<"
if self.phase == '*':
s += "Phases: all; "
if self.atom is not None:
if ":" in str(self.atom):
s += "Rigid body" + str(self.atom) + "; "
else:
s += "Atom #" + str(self.atom) + "; "
elif self.phase is not None:
ph = _lookup(PhaseRanIdLookup,self.phase)
s += "Phase: rId=" + str(self.phase) + " (#"+ ph + "); "
if self.atom == '*':
s += "Atoms: all; "
elif ":" in self(self.atom):
s += "Rigid body" + str(self.atom) + "; "
elif self.atom is not None:
s += "Atom rId=" + str(self.atom)
if ph in AtomRanIdLookup:
s += " (#" + AtomRanIdLookup[ph].get(self.atom,'?') + "); "
else:
s += " (#? -- not found!); "
if self.histogram == '*':
s += "Histograms: all; "
elif self.histogram is not None:
hist = _lookup(HistRanIdLookup,self.histogram)
s += "Histogram: rId=" + str(self.histogram) + " (#"+ hist + "); "
s += 'Variable name="' + str(self.name) + '">'
return s+" ("+self.varname()+")"
def __eq__(self, other):
if type(other) is type(self):
return (self.phase == other.phase and
self.histogram == other.histogram and
self.name == other.name and
self.atom == other.atom)
return False
def _show(self):
'For testing, shows the current lookup table'
print 'phases', self.IDdict['phases']
print 'hists', self.IDdict['hists']
print 'atomDict', self.IDdict['atoms']
#==========================================================================
# shortcut routines
exp = np.exp
sind = sin = s = lambda x: np.sin(x*np.pi/180.)
cosd = cos = c = lambda x: np.cos(x*np.pi/180.)
tand = tan = t = lambda x: np.tan(x*np.pi/180.)
sqrt = sq = lambda x: np.sqrt(x)
pi = lambda: np.pi
[docs]class ExpressionObj(object):
'''Defines an object with a user-defined expression, to be used for
secondary fits or restraints. Object is created null, but is changed
using :meth:`LoadExpression`. This contains only the minimum
information that needs to be stored to save and load the expression
and how it is mapped to GSAS-II variables.
'''
def __init__(self):
self.expression = ''
'The expression as a text string'
self.assgnVars = {}
'''A dict where keys are label names in the expression mapping to a GSAS-II
variable. The value a G2 variable name.
Note that the G2 variable name may contain a wild-card and correspond to
multiple values.
'''
self.freeVars = {}
'''A dict where keys are label names in the expression mapping to a free
parameter. The value is a list with:
* a name assigned to the parameter
* a value for to the parameter and
* a flag to determine if the variable is refined.
'''
self.depVar = None
self.lastError = ('','')
'''Shows last encountered error in processing expression
(list of 1-3 str values)'''
[docs] def LoadExpression(self,expr,exprVarLst,varSelect,varName,varValue,varRefflag):
'''Load the expression and associated settings into the object. Raises
an exception if the expression is not parsed, if not all functions
are defined or if not all needed parameter labels in the expression
are defined.
This will not test if the variable referenced in these definitions
are actually in the parameter dictionary. This is checked when the
computation for the expression is done in :meth:`SetupCalc`.
:param str expr: the expression
:param list exprVarLst: parameter labels found in the expression
:param dict varSelect: this will be 0 for Free parameters
and non-zero for expression labels linked to G2 variables.
:param dict varName: Defines a name (str) associated with each free parameter
:param dict varValue: Defines a value (float) associated with each free parameter
:param dict varRefflag: Defines a refinement flag (bool)
associated with each free parameter
'''
self.expression = expr
self.compiledExpr = None
self.freeVars = {}
self.assgnVars = {}
for v in exprVarLst:
if varSelect[v] == 0:
self.freeVars[v] = [
varName.get(v),
varValue.get(v),
varRefflag.get(v),
]
else:
self.assgnVars[v] = varName[v]
self.CheckVars()
[docs] def EditExpression(self,exprVarLst,varSelect,varName,varValue,varRefflag):
'''Load the expression and associated settings from the object into
arrays used for editing.
:param list exprVarLst: parameter labels found in the expression
:param dict varSelect: this will be 0 for Free parameters
and non-zero for expression labels linked to G2 variables.
:param dict varName: Defines a name (str) associated with each free parameter
:param dict varValue: Defines a value (float) associated with each free parameter
:param dict varRefflag: Defines a refinement flag (bool)
associated with each free parameter
:returns: the expression as a str
'''
for v in self.freeVars:
varSelect[v] = 0
varName[v] = self.freeVars[v][0]
varValue[v] = self.freeVars[v][1]
varRefflag[v] = self.freeVars[v][2]
for v in self.assgnVars:
varSelect[v] = 1
varName[v] = self.assgnVars[v]
return self.expression
[docs] def GetVaried(self):
'Returns the names of the free parameters that will be refined'
return ["::"+self.freeVars[v][0] for v in self.freeVars if self.freeVars[v][2]]
[docs] def GetVariedVarVal(self):
'Returns the names and values of the free parameters that will be refined'
return [("::"+self.freeVars[v][0],self.freeVars[v][1]) for v in self.freeVars if self.freeVars[v][2]]
[docs] def UpdateVariedVars(self,varyList,values):
'Updates values for the free parameters (after a refinement); only updates refined vars'
for v in self.freeVars:
if not self.freeVars[v][2]: continue
if "::"+self.freeVars[v][0] not in varyList: continue
indx = varyList.index("::"+self.freeVars[v][0])
self.freeVars[v][1] = values[indx]
[docs] def GetIndependentVars(self):
'Returns the names of the required independent parameters used in expression'
return [self.assgnVars[v] for v in self.assgnVars]
[docs] def CheckVars(self):
'''Check that the expression can be parsed, all functions are
defined and that input loaded into the object is internally
consistent. If not an Exception is raised.
:returns: a dict with references to packages needed to
find functions referenced in the expression.
'''
ret = self.ParseExpression(self.expression)
if not ret:
raise Exception("Expression parse error")
exprLblList,fxnpkgdict = ret
# check each var used in expression is defined
defined = self.assgnVars.keys() + self.freeVars.keys()
notfound = []
for var in exprLblList:
if var not in defined:
notfound.append(var)
if notfound:
msg = 'Not all variables defined'
msg1 = 'The following variables were not defined: '
msg2 = ''
for var in notfound:
if msg: msg += ', '
msg += var
self.lastError = (msg1,' '+msg2)
raise Exception(msg)
return fxnpkgdict
[docs] def ParseExpression(self,expr):
'''Parse an expression and return a dict of called functions and
the variables used in the expression. Returns None in case an error
is encountered. If packages are referenced in functions, they are loaded
and the functions are looked up into the modules global
workspace.
Note that no changes are made to the object other than
saving an error message, so that this can be used for testing prior
to the save.
:returns: a list of used variables
'''
self.lastError = ('','')
import ast
def FindFunction(f):
'''Find the object corresponding to function f
:param str f: a function name such as 'numpy.exp'
:returns: (pkgdict,pkgobj) where pkgdict contains a dict
that defines the package location(s) and where pkgobj
defines the object associated with the function.
If the function is not found, pkgobj is None.
'''
df = f.split('.')
pkgdict = {}
# no listed package, try in current namespace
if len(df) == 1:
try:
fxnobj = eval(f)
return pkgdict,fxnobj
except (AttributeError, NameError):
return None,None
else:
try:
fxnobj = eval(f)
pkgdict[df[0]] = eval(df[0])
return pkgdict,fxnobj
except (AttributeError, NameError):
pass
# includes a package, lets try to load the packages
pkgname = ''
path = sys.path
for pkg in f.split('.')[:-1]: # if needed, descend down the tree
if pkgname:
pkgname += '.' + pkg
else:
pkgname = pkg
fp = None
try:
fp, fppath,desc = imp.find_module(pkg,path)
pkgobj = imp.load_module(pkg,fp,fppath,desc)
pkgdict[pkgname] = pkgobj
path = [fppath]
except Exception as msg:
print('load of '+pkgname+' failed with error='+str(msg))
return {},None
finally:
if fp: fp.close()
try:
#print 'before',pkgdict.keys()
fxnobj = eval(f,globals(),pkgdict)
#print 'after 1',pkgdict.keys()
#fxnobj = eval(f,pkgdict)
#print 'after 2',pkgdict.keys()
return pkgdict,fxnobj
except:
continue
return None # not found
def ASTtransverse(node,fxn=False):
'''Transverse a AST-parsed expresson, compiling a list of variables
referenced in the expression. This routine is used recursively.
:returns: varlist,fxnlist where
varlist is a list of referenced variable names and
fxnlist is a list of used functions
'''
varlist = []
fxnlist = []
if isinstance(node, list):
for b in node:
v,f = ASTtransverse(b,fxn)
varlist += v
fxnlist += f
elif isinstance(node, ast.AST):
for a, b in ast.iter_fields(node):
if isinstance(b, ast.AST):
if a == 'func':
fxnlist += ['.'.join(ASTtransverse(b,True)[0])]
continue
v,f = ASTtransverse(b,fxn)
varlist += v
fxnlist += f
elif isinstance(b, list):
v,f = ASTtransverse(b,fxn)
varlist += v
fxnlist += f
elif node.__class__.__name__ == "Name":
varlist += [b]
elif fxn and node.__class__.__name__ == "Attribute":
varlist += [b]
return varlist,fxnlist
try:
exprast = ast.parse(expr)
except SyntaxError as err:
s = ''
import traceback
for i in traceback.format_exc().splitlines()[-3:-1]:
if s: s += "\n"
s += str(i)
self.lastError = ("Error parsing expression:",s)
return
# find the variables & functions
v,f = ASTtransverse(exprast)
varlist = sorted(list(set(v)))
fxnlist = list(set(f))
pkgdict = {}
# check the functions are defined
for fxn in fxnlist:
fxndict,fxnobj = FindFunction(fxn)
if not fxnobj:
self.lastError = ("Error: Invalid function",fxn,
"is not defined")
return
if not hasattr(fxnobj,'__call__'):
self.lastError = ("Error: Not a function.",fxn,
"cannot be called as a function")
return
pkgdict.update(fxndict)
return varlist,pkgdict
[docs] def SetDepVar(self,var):
'Set the dependent variable, if used'
self.depVar = var
#==========================================================================
[docs]class ExpressionCalcObj(object):
'''An object used to evaluate an expression from a :class:`ExpressionObj`
object.
:param ExpressionObj exprObj: a :class:`~ExpressionObj` expression object with
an expression string and mappings for the parameter labels in that object.
'''
def __init__(self,exprObj):
self.eObj = exprObj
'The expression and mappings; a :class:`ExpressionObj` object'
self.compiledExpr = None
'The expression as compiled byte-code'
self.exprDict = {}
'''dict that defines values for labels used in expression and packages
referenced by functions
'''
self.lblLookup = {}
'''Lookup table that specifies the expression label name that is
tied to a particular GSAS-II parameters in the parmDict.
'''
self.fxnpkgdict = {}
'''a dict with references to packages needed to
find functions referenced in the expression.
'''
self.varLookup = {}
'''Lookup table that specifies the GSAS-II variable(s)
indexed by the expression label name. (Used for only for diagnostics
not evaluation of expression.)
'''
# Patch: for old-style expressions with a (now removed step size)
for v in self.eObj.assgnVars:
if not isinstance(self.eObj.assgnVars[v], basestring):
self.eObj.assgnVars[v] = self.eObj.assgnVars[v][0]
[docs] def SetupCalc(self,parmDict):
'''Do all preparations to use the expression for computation.
Adds the free parameter values to the parameter dict (parmDict).
'''
self.fxnpkgdict = self.eObj.CheckVars()
# all is OK, compile the expression
self.compiledExpr = compile(self.eObj.expression,'','eval')
# look at first value in parmDict to determine its type
parmsInList = True
for key in parmDict:
val = parmDict[key]
if isinstance(val, basestring):
parmsInList = False
break
try: # check if values are in lists
val = parmDict[key][0]
except (TypeError,IndexError):
parmsInList = False
break
# set up the dicts needed to speed computations
self.exprDict = {}
self.lblLookup = {}
self.varLookup = {}
for v in self.eObj.freeVars:
varname = self.eObj.freeVars[v][0]
varname = "::" + varname.lstrip(':').replace(' ','_').replace(':',';')
self.lblLookup[varname] = v
self.varLookup[v] = varname
if parmsInList:
parmDict[varname] = [self.eObj.freeVars[v][1],self.eObj.freeVars[v][2]]
else:
parmDict[varname] = self.eObj.freeVars[v][1]
self.exprDict[v] = self.eObj.freeVars[v][1]
for v in self.eObj.assgnVars:
varname = self.eObj.assgnVars[v]
if '*' in varname:
varlist = LookupWildCard(varname,parmDict.keys())
if len(varlist) == 0:
raise Exception,"No variables match "+str(v)
for var in varlist:
self.lblLookup[var] = v
if parmsInList:
self.exprDict[v] = np.array([parmDict[var][0] for var in varlist])
else:
self.exprDict[v] = np.array([parmDict[var] for var in varlist])
self.varLookup[v] = [var for var in varlist]
elif varname in parmDict:
self.lblLookup[varname] = v
self.varLookup[v] = varname
if parmsInList:
self.exprDict[v] = parmDict[varname][0]
else:
self.exprDict[v] = parmDict[varname]
else:
raise Exception,"No value for variable "+str(v)
self.exprDict.update(self.fxnpkgdict)
[docs] def UpdateVars(self,varList,valList):
'''Update the dict for the expression with a set of values
:param list varList: a list of variable names
:param list valList: a list of corresponding values
'''
for var,val in zip(varList,valList):
self.exprDict[self.lblLookup.get(var,'undefined: '+var)] = val
[docs] def UpdateDict(self,parmDict):
'''Update the dict for the expression with values in a dict
:param list parmDict: a dict of values some of which may be in use here
'''
for var in parmDict:
if var in self.lblLookup:
self.exprDict[self.lblLookup[var]] = parmDict[var]
[docs] def EvalExpression(self):
'''Evaluate an expression. Note that the expression
and mapping are taken from the :class:`ExpressionObj` expression object
and the parameter values were specified in :meth:`SetupCalc`.
:returns: a single value for the expression. If parameter
values are arrays (for example, from wild-carded variable names),
the sum of the resulting expression is returned.
For example, if the expression is ``'A*B'``,
where A is 2.0 and B maps to ``'1::Afrac:*'``, which evaluates to::
[0.5, 1, 0.5]
then the result will be ``4.0``.
'''
if self.compiledExpr is None:
raise Exception,"EvalExpression called before SetupCalc"
val = eval(self.compiledExpr,globals(),self.exprDict)
if not np.isscalar(val):
val = np.sum(val)
return val
class G2Exception(Exception):
def __init__(self,msg):
self.msg = msg
def __str__(self):
return repr(self.msg)
if __name__ == "__main__":
# test equation evaluation
def showEQ(calcobj):
print 50*'='
print calcobj.eObj.expression,'=',calcobj.EvalExpression()
for v in sorted(calcobj.varLookup):
print " ",v,'=',calcobj.exprDict[v],'=',calcobj.varLookup[v]
# print ' Derivatives'
# for v in calcobj.derivStep.keys():
# print ' d(Expr)/d('+v+') =',calcobj.EvalDeriv(v)
obj = ExpressionObj()
obj.expression = "A*np.exp(B)"
obj.assgnVars = {'B': '0::Afrac:1'}
obj.freeVars = {'A': [u'A', 0.5, True]}
#obj.CheckVars()
parmDict2 = {'0::Afrac:0':[0.0,True], '0::Afrac:1': [1.0,False]}
calcobj = ExpressionCalcObj(obj)
calcobj.SetupCalc(parmDict2)
showEQ(calcobj)
obj.expression = "A*np.exp(B)"
obj.assgnVars = {'B': '0::Afrac:*'}
obj.freeVars = {'A': [u'Free Prm A', 0.5, True]}
#obj.CheckVars()
parmDict1 = {'0::Afrac:0':1.0, '0::Afrac:1': 1.0}
calcobj = ExpressionCalcObj(obj)
calcobj.SetupCalc(parmDict1)
showEQ(calcobj)
calcobj.SetupCalc(parmDict2)
showEQ(calcobj)
