Index: /trunk/GSASIIobj.py
===================================================================
--- /trunk/GSASIIobj.py (revision 4637)
+++ /trunk/GSASIIobj.py (revision 4638)
@@ -120,28 +120,28 @@
key sub-key explanation
============= =============== ====================================================
-newCellDict \ (dict) ith lattice parameters computed by
+newCellDict \\ (dict) ith lattice parameters computed by
:func:`GSASIIstrMath.GetNewCellParms`
-title \ (str) Name of gpx file(?)
-variables \ (list) Values for all N refined variables
+title \\ (str) Name of gpx file(?)
+variables \\ (list) Values for all N refined variables
(list of float values, length N,
ordered to match varyList)
-sig \ (list) Uncertainty values for all N refined variables
+sig \\ (list) Uncertainty values for all N refined variables
(list of float values, length N,
ordered to match varyList)
-varyList \ (list of str values, length N) List of directly refined variables
+varyList \\ (list of str values, length N) List of directly refined variables
-newAtomDict \ (dict) atom position values computed in
+newAtomDict \\ (dict) atom position values computed in
:func:`GSASIIstrMath.ApplyXYZshifts`
-Rvals \ (dict) R-factors, GOF, Marquardt value for last
+Rvals \\ (dict) R-factors, GOF, Marquardt value for last
refinement cycle
-\ Nobs (int) Number of observed data points
-\ Rwp (float) overall weighted profile R-factor (%)
-\ chisq (float) :math:`\sum w*(I_{obs}-I_{calc})^2`
+\\ Nobs (int) Number of observed data points
+\\ Rwp (float) overall weighted profile R-factor (%)
+\\ chisq (float) :math:`\sum w*(I_{obs}-I_{calc})^2`
for all data.
Note: this is not the reduced :math:`\chi^2`.
-\ lamMax (float) Marquardt value applied to Hessian diagonal
-\ GOF (float) The goodness-of-fit, aka square root of
+\\ lamMax (float) Marquardt value applied to Hessian diagonal
+\\ GOF (float) The goodness-of-fit, aka square root of
the reduced chi squared.
-covMatrix \ (np.array) The (NxN) covVariance matrix
+covMatrix \\ (np.array) The (NxN) covVariance matrix
============= =============== ====================================================
@@ -163,15 +163,15 @@
key sub-key explanation
========== =============== =====================================================================================================
-General \ (dict) Overall information for the phase
- \ 3Dproj (list of str) projections for 3D pole distribution plots
- \ AngleRadii (list of floats) Default radius for each atom used to compute
+General \\ (dict) Overall information for the phase
+ \\ 3Dproj (list of str) projections for 3D pole distribution plots
+ \\ AngleRadii (list of floats) Default radius for each atom used to compute
interatomic angles
- \ AtomMass (list of floats) Masses for atoms
- \ AtomPtrs (list of int) four locations (cx,ct,cs & cu) to use to pull info
+ \\ AtomMass (list of floats) Masses for atoms
+ \\ AtomPtrs (list of int) four locations (cx,ct,cs & cu) to use to pull info
from the atom records
- \ AtomTypes (llist of str) Atom types
- \ BondRadii (list of floats) Default radius for each atom used to compute
+ \\ AtomTypes (llist of str) Atom types
+ \\ BondRadii (list of floats) Default radius for each atom used to compute
interatomic distances
- \ Cell Unit cell parameters & ref. flag
+ \\ Cell Unit cell parameters & ref. flag
(list with 8 items. All but first item are float.)
@@ -180,9 +180,9 @@
4-6: alpha, beta & gamma, (degrees)
7: volume (:math:`\\AA^3`)
- \ Color (list of (r,b,g) triplets) Colors for atoms
- \ Compare (dict) Polygon comparison parameters
- \ Data plot type (str) data plot type ('Mustrain', 'Size' or
+ \\ Color (list of (r,b,g) triplets) Colors for atoms
+ \\ Compare (dict) Polygon comparison parameters
+ \\ Data plot type (str) data plot type ('Mustrain', 'Size' or
'Preferred orientation') for powder data
- \ DisAglCtls (dDict) with distance/angle search controls,
+ \\ DisAglCtls (dDict) with distance/angle search controls,
which has keys 'Name', 'AtomTypes',
'BondRadii', 'AngleRadii' which are as above
@@ -191,81 +191,81 @@
a multiplier for bond and angle search range
[typically (0.85,0.85)].
- \ F000X (float) x-ray F(000) intensity
- \ F000N (float) neutron F(000) intensity
- \ Flip (dict) Charge flip controls
- \ HydIds (dict) geometrically generated hydrogen atoms
- \ Isotope (dict) Isotopes for each atom type
- \ Isotopes (dict) Scattering lengths for each isotope
+ \\ F000X (float) x-ray F(000) intensity
+ \\ F000N (float) neutron F(000) intensity
+ \\ Flip (dict) Charge flip controls
+ \\ HydIds (dict) geometrically generated hydrogen atoms
+ \\ Isotope (dict) Isotopes for each atom type
+ \\ Isotopes (dict) Scattering lengths for each isotope
combination for each element in phase
- \ MCSA controls (dict) Monte Carlo-Simulated Annealing controls
- \ Map (dict) Map parameters
- \ Mass (float) Mass of unit cell contents in g/mol
- \ Modulated (bool) True if phase modulated
- \ Mydir (str) Directory of current .gpx file
- \ Name (str) Phase name
- \ NoAtoms (dict) Number of atoms per unit cell of each type
- \ POhkl (list) March-Dollase preferred orientation direction
- \ Pawley dmin (float) maximum Q (as d-space) to use for Pawley extraction
- \ Pawley dmax (float) minimum Q (as d-space) to use for Pawley extraction
- \ Pawley neg wt (float) Restraint value for negative Pawley intensities
- \ SGData (object) Space group details as a
+ \\ MCSA controls (dict) Monte Carlo-Simulated Annealing controls
+ \\ Map (dict) Map parameters
+ \\ Mass (float) Mass of unit cell contents in g/mol
+ \\ Modulated (bool) True if phase modulated
+ \\ Mydir (str) Directory of current .gpx file
+ \\ Name (str) Phase name
+ \\ NoAtoms (dict) Number of atoms per unit cell of each type
+ \\ POhkl (list) March-Dollase preferred orientation direction
+ \\ Pawley dmin (float) maximum Q (as d-space) to use for Pawley extraction
+ \\ Pawley dmax (float) minimum Q (as d-space) to use for Pawley extraction
+ \\ Pawley neg wt (float) Restraint value for negative Pawley intensities
+ \\ SGData (object) Space group details as a
:ref:`space group (SGData) `
object, as defined in :func:`GSASIIspc.SpcGroup`.
- \ SH Texture (dict) Spherical harmonic preferred orientation parameters
- \ Super (int) dimension of super group (0,1 only)
- \ Type (str) phase type (e.g. 'nuclear')
- \ Z (dict) Atomic numbers for each atom type
- \ doDysnomia (bool) flag for max ent map modification via Dysnomia
- \ doPawley (bool) Flag for Pawley intensity extraction
- \ vdWRadii (dict) Van der Waals radii for each atom type
-ranId \ (int) unique random number Id for phase
-pId \ (int) Phase Id number for current project.
-Atoms \ (list of lists) Atoms in phase as a list of lists. The outer list
+ \\ SH Texture (dict) Spherical harmonic preferred orientation parameters
+ \\ Super (int) dimension of super group (0,1 only)
+ \\ Type (str) phase type (e.g. 'nuclear')
+ \\ Z (dict) Atomic numbers for each atom type
+ \\ doDysnomia (bool) flag for max ent map modification via Dysnomia
+ \\ doPawley (bool) Flag for Pawley intensity extraction
+ \\ vdWRadii (dict) Van der Waals radii for each atom type
+ranId \\ (int) unique random number Id for phase
+pId \\ (int) Phase Id number for current project.
+Atoms \\ (list of lists) 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 ` description.
-Drawing \ (dict) Display parameters
-\ Atoms (list of lists) with an entry for each atom that is drawn
-\ Plane (list) Controls for contour density plane display
-\ Quaternion (4 element np.array) Viewing quaternion
-\ Zclip (float) clipping distance in :math:`\\AA`
-\ Zstep (float) Step to de/increase Z-clip
-\ atomPtrs (list) positions of x, type, site sym, ADP flag in Draw Atoms
-\ backColor (list) background for plot as and R,G,B triplet
+Drawing \\ (dict) Display parameters
+\\ Atoms (list of lists) with an entry for each atom that is drawn
+\\ Plane (list) Controls for contour density plane display
+\\ Quaternion (4 element np.array) Viewing quaternion
+\\ Zclip (float) clipping distance in :math:`\\AA`
+\\ Zstep (float) Step to de/increase Z-clip
+\\ atomPtrs (list) positions of x, type, site sym, ADP flag in Draw Atoms
+\\ backColor (list) background for plot as and R,G,B triplet
(default = [0, 0, 0], black).
-\ ballScale (float) Radius of spheres in ball-and-stick display
-\ bondList (dict) Bonds
-\ bondRadius (float) Radius of binds in :math:`\\AA`
-\ cameraPos (float) Viewing position in :math:`\\AA` for plot
-\ contourLevel (float) map contour level in :math:`e/\\AA^3`
-\ contourMax (float) map contour maximum
-\ depthFog (bool) True if use depthFog on plot - set currently as False
-\ ellipseProb (float) Probability limit for display of thermal
+\\ ballScale (float) Radius of spheres in ball-and-stick display
+\\ bondList (dict) Bonds
+\\ bondRadius (float) Radius of binds in :math:`\\AA`
+\\ cameraPos (float) Viewing position in :math:`\\AA` for plot
+\\ contourLevel (float) map contour level in :math:`e/\\AA^3`
+\\ contourMax (float) map contour maximum
+\\ depthFog (bool) True if use depthFog on plot - set currently as False
+\\ ellipseProb (float) Probability limit for display of thermal
ellipsoids in % .
-\ magMult (float) multiplier for magnetic moment arrows
-\ mapSize (float) x & y dimensions of contourmap (fixed internally)
-\ modelView (4,4 array) from openGL drawing transofmation matrix
-\ oldxy (list with two floats) previous view point
-\ radiusFactor (float) Distance ratio for searching for bonds. Bonds
+\\ magMult (float) multiplier for magnetic moment arrows
+\\ mapSize (float) x & y dimensions of contourmap (fixed internally)
+\\ modelView (4,4 array) from openGL drawing transofmation matrix
+\\ oldxy (list with two floats) previous view point
+\\ radiusFactor (float) 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.
-\ selectedAtoms (list of int values) List of selected atoms
-\ showABC (bool) Flag to show view point triplet. True=show.
-\ showHydrogen (bool) Flag to control plotting of H atoms.
-\ showRigidBodies (bool) Flag to highlight rigid body placement
-\ showSlice (bool) flag to show contour map
-\ sizeH (float) Size ratio for H atoms
-\ unitCellBox (bool) Flag to control display of the unit cell.
-\ vdwScale (float) Multiplier of van der Waals radius for display of vdW spheres.
-\ viewDir (np.array with three floats) cartesian viewing direction
-\ viewPoint (list of lists) First item in list is [x,y,z]
+\\ selectedAtoms (list of int values) List of selected atoms
+\\ showABC (bool) Flag to show view point triplet. True=show.
+\\ showHydrogen (bool) Flag to control plotting of H atoms.
+\\ showRigidBodies (bool) Flag to highlight rigid body placement
+\\ showSlice (bool) flag to show contour map
+\\ sizeH (float) Size ratio for H atoms
+\\ unitCellBox (bool) Flag to control display of the unit cell.
+\\ vdwScale (float) Multiplier of van der Waals radius for display of vdW spheres.
+\\ viewDir (np.array with three floats) cartesian viewing direction
+\\ 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])
-RBModels \ Rigid body assignments (note Rigid body definitions
+RBModels \\ Rigid body assignments (note Rigid body definitions
are stored in their own main top-level tree entry.)
-RMC \ (dict) RMCProfile & rmcfull controls
-Pawley ref \ (list) Pawley reflections
-Histograms \ (dict of dicts) The key for the outer dict is
+RMC \\ (dict) RMCProfile & rmcfull controls
+Pawley ref \\ (list) Pawley reflections
+Histograms \\ (dict of dicts) The key for the outer dict is
the histograms tied to this phase. The inner
dict contains the combined phase/histogram
@@ -273,16 +273,16 @@
size and strain parameters. The following are the
keys to the inner dict. (dict)
-\ Babinet (dict) For protein crystallography. Dictionary with two
+\\ Babinet (dict) For protein crystallography. Dictionary with two
entries, 'BabA', 'BabU'
-\ Extinction (list of float, bool) Extinction parameter
-\ Flack (list of [float, bool]) Flack parameter & refine flag
-\ HStrain (list of two lists) Hydrostatic strain. The first is
+\\ Extinction (list of float, bool) Extinction parameter
+\\ Flack (list of [float, bool]) Flack parameter & refine flag
+\\ HStrain (list of two lists) Hydrostatic strain. The first is
a list of the HStrain parameters (1, 2, 3, 4, or 6
depending on unit cell), the second is a list of boolean
refinement parameters (same length)
-\ Histogram (str) The name of the associated histogram
-\ Layer Disp (list of [float, bool]) Layer displacement in beam direction & refine flag
-\ LeBail (bool) Flag for LeBail extraction
-\ Mustrain (list) Microstrain parameters, in order:
+\\ Histogram (str) The name of the associated histogram
+\\ Layer Disp (list of [float, bool]) Layer displacement in beam direction & refine flag
+\\ LeBail (bool) Flag for LeBail extraction
+\\ Mustrain (list) Microstrain parameters, in order:
0. Type, one of u'isotropic', u'uniaxial', u'generalized'
@@ -292,5 +292,5 @@
4. Generalized mustrain parameters - list of 2-6 floats, depending on space group
5. Generalized refinement flags - list of bools, corresponding to the parameters of (4)
-\ Pref.Ori. (list) Preferred Orientation. List of eight parameters.
+\\ Pref.Ori. (list) Preferred Orientation. List of eight parameters.
Items marked SH are only used for Spherical Harmonics.
@@ -303,6 +303,6 @@
6. (list) SH
7. (float) SH
-\ Scale (list of [float, bool]) Phase fraction & refine flag
-\ Size List of crystallite size parameters, in order:
+\\ Scale (list of [float, bool]) Phase fraction & refine flag
+\\ Size List of crystallite size parameters, in order:
0. (str) Type, one of u'isotropic', u'uniaxial', u'ellipsoidal'
@@ -312,7 +312,7 @@
4. (list) Ellipsoidal size parameters - list of 6 floats
5. (list) Ellipsoidal refinement flags - list of bools, corresponding to the parameters of (4)
-\ Use (bool) True if this histogram is to be used in refinement
-\ newLeBail (bool) Whether to perform a new LeBail extraction
-MCSA \ (dict) Monte-Carlo simulated annealing parameters
+\\ Use (bool) True if this histogram is to be used in refinement
+\\ newLeBail (bool) Whether to perform a new LeBail extraction
+MCSA \\ (dict) Monte-Carlo simulated annealing parameters
========== =============== =====================================================================================================
@@ -337,30 +337,30 @@
========== =============== ====================================================
Vector RBId (dict of dict) vector rigid bodies
-\ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type
-\ RBname (str) Name assigned by user to rigid body
-\ VectMag (list) vector magnitudes in :math:`\\AA`
-\ rbXYZ (list of 3 float Cartesian coordinates for Vector rigid body )
-\ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
+\\ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type
+\\ RBname (str) Name assigned by user to rigid body
+\\ VectMag (list) vector magnitudes in :math:`\\AA`
+\\ rbXYZ (list of 3 float Cartesian coordinates for Vector rigid body )
+\\ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
definition, use center of atoms flag
-\ VectRef (list of bool refinement flags for VectMag values )
-\ rbTypes (list of str) Atom types for each atom in rigid body
-\ rbVect (list of lists) Cartesian vectors for each translation used to build rigid body
-\ useCount (int) Number of times rigid body is used in any structure
+\\ VectRef (list of bool refinement flags for VectMag values )
+\\ rbTypes (list of str) Atom types for each atom in rigid body
+\\ rbVect (list of lists) Cartesian vectors for each translation used to build rigid body
+\\ useCount (int) Number of times rigid body is used in any structure
Residue RBId (dict of dict) residue rigid bodies
-\ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type
-\ RBname (str) Name assigned by user to rigid body
-\ rbXYZ (list of 3 float) Cartesian coordinates for Residue rigid body
-\ rbTypes (list of str) Atom types for each atom in rigid body
-\ atNames (list of str) Names of each atom in rigid body (e.g. C1,N2...)
-\ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
+\\ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type
+\\ RBname (str) Name assigned by user to rigid body
+\\ rbXYZ (list of 3 float) Cartesian coordinates for Residue rigid body
+\\ rbTypes (list of str) Atom types for each atom in rigid body
+\\ atNames (list of str) Names of each atom in rigid body (e.g. C1,N2...)
+\\ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin
definition, use center of atoms flag
-\ rbSeq (list) Orig,Piv,angle,Riding : definition of internal rigid body
+\\ rbSeq (list) Orig,Piv,angle,Riding : 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 (int)Number of times rigid body is used in any structure
-RBIds \ (dict) unique Ids generated upon creation of each rigid body
-\ Vector (list) Ids for each Vector rigid body
-\ Residue (list) Ids for each Residue rigid body
+\\ SelSeq (int,int) used by SeqSizer to identify objects
+\\ useCount (int)Number of times rigid body is used in any structure
+RBIds \\ (dict) unique Ids generated upon creation of each rigid body
+\\ Vector (list) Ids for each Vector rigid body
+\\ Residue (list) Ids for each Residue rigid body
========== =============== ====================================================
@@ -557,21 +557,21 @@
key sub-key explanation
====================== =============== ===========================================================
-Comments \ (list of str) Text strings extracted from the original powder
+Comments \\ (list of str) Text strings extracted from the original powder
data header. These cannot be changed by the user;
it may be empty.
-Limits \ (list) two two element lists, as [[Ld,Hd],[L,H]]
+Limits \\ (list) 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 \ (dict of dicts) with an entry for each phase in the
+Reflection Lists \\ (dict of dicts) 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 `
description.
-Instrument Parameters \ (dict) The instrument parameters uses different dicts
+Instrument Parameters \\ (dict) The instrument parameters uses different dicts
for the constant wavelength (CW) and time-of-flight (TOF)
cases. See below for the descriptions of each.
-wtFactor \ (float) A weighting factor to increase or decrease
+wtFactor \\ (float) A weighting factor to increase or decrease
the leverage of data in the histogram .
A value of 1.0 weights the data with their
@@ -579,5 +579,5 @@
increases the weighting of the data (equivalent
to decreasing the uncertainties).
-Sample Parameters \ (dict) Parameters that describe how
+Sample Parameters \\ (dict) Parameters that describe how
the data were collected, as listed
below. Refinable parameters are a list containing
@@ -585,36 +585,36 @@
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
+\\ 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
+\\ 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 -
+\\ SurfaceRoughB Surface roughness parameter B (refinable -
only valid for Bragg-Brentano geometry)
-\ DisplaceX, Sample displacement from goniometer center
+\\ 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.
+\\ Phi, Chi, Goniometer sample setting angles, in degrees.
Omega
-\ Gonio. radius Radius of the diffractometer in mm
-\ InstrName (str) A name for the instrument, used in preparing
+\\ Gonio. radius Radius of the diffractometer in mm
+\\ InstrName (str) A name for the instrument, used in preparing
a CIF .
-\ Force, Variables that describe how the measurement
+\\ Force, Variables that describe how the measurement
Temperature, was performed. Not used directly in
Humidity, any computations.
Pressure,
Voltage
-\ ranId (int) The random-number Id for the histogram
+\\ ranId (int) The random-number Id for the histogram
(same value as where top-level key is ranId)
-\ Type (str) Type of diffraction data, may be 'Debye-Scherrer'
+\\ Type (str) Type of diffraction data, may be 'Debye-Scherrer'
or 'Bragg-Brentano' .
-hId \ (int) The number assigned to the histogram when
+hId \\ (int) The number assigned to the histogram when
the project is loaded or edited (can change)
-ranId \ (int) A random number id for the histogram
+ranId \\ (int) A random number id for the histogram
that does not change
-Background \ (list) The background is stored as a list with where
+Background \\ (list) 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
@@ -622,5 +622,5 @@
Debye diffuse terms and background peaks.
(TODO: this needs to be expanded.)
-Data \ (list) The data consist of a list of 6 np.arrays
+Data \\ (list) The data consist of a list of 6 np.arrays
containing in order:
@@ -658,26 +658,26 @@
* 'PXC' for constant wavelength x-ray
* 'PNC' for constant wavelength neutron
-\ Bank [*] (int) Data set number in a multidata file (usually 1)
-\ Lam (float) Specifies a wavelength in :math:`\\AA`
-\ Lam1 [*] (float) Specifies the primary wavelength in
+\\ Bank [*] (int) Data set number in a multidata file (usually 1)
+\\ Lam (float) Specifies a wavelength in :math:`\\AA`
+\\ Lam1 [*] (float) Specifies the primary wavelength in
:math:`\\AA`, used in place of Lam
when an :math:`\\alpha_1, \\alpha_2`
source is used.
-\ Lam2 [*] (float) Specifies the secondary wavelength in
+\\ Lam2 [*] (float) Specifies the secondary wavelength in
:math:`\\AA`, used with Lam1
-\ I(L2)/I(L1) (float) Ratio of Lam2 to Lam1, used with Lam1
-\ Zero (float) Two-theta zero correction in *degrees*
-\ Azimuth [*] (float) Azimuthal setting angle for data recorded with differing setting angles
-\ U, V, W (float) Cagliotti profile coefficients
+\\ I(L2)/I(L1) (float) Ratio of Lam2 to Lam1, used with Lam1
+\\ Zero (float) Two-theta zero correction in *degrees*
+\\ Azimuth [*] (float) Azimuthal setting angle for data recorded with differing setting angles
+\\ U, V, W (float) Cagliotti profile coefficients
for Gaussian instrumental broadening, where the
FWHM goes as
:math:`U \\tan^2\\theta + V \\tan\\theta + W`
-\ X, Y, Z (float) Cauchy (Lorentzian) instrumental broadening coefficients
-\ SH/L (float) Variant of the Finger-Cox-Jephcoat asymmetric
+\\ X, Y, Z (float) Cauchy (Lorentzian) instrumental broadening coefficients
+\\ SH/L (float) Variant of the Finger-Cox-Jephcoat asymmetric
peak broadening ratio. Note that this is the
sum of S/L and H/L where S is
sample height, H is the slit height and
L is the goniometer diameter.
-\ Polariz. (float) Polarization coefficient.
+\\ Polariz. (float) Polarization coefficient.
Instrument Parameters[1] (empty dict)
======================== =============== ===========================================================
@@ -707,21 +707,21 @@
Instrument Parameters[0] Type [*] (str) Histogram type:
* 'PNT' for time of flight neutron
-\ Bank (int) Data set number in a multidata file
-\ 2-theta [*] (float) Nominal scattering angle for the detector
-\ fltPath [*] (float) Total flight path source-sample-detector
-\ Azimuth [*] (float) Azimuth angle for detector right hand rotation
+\\ Bank (int) Data set number in a multidata file
+\\ 2-theta [*] (float) Nominal scattering angle for the detector
+\\ fltPath [*] (float) Total flight path source-sample-detector
+\\ Azimuth [*] (float) Azimuth angle for detector right hand rotation
from horizontal away from source
-\ difC,difA, (float) Diffractometer constants for conversion of d-spacing to TOF
+\\ difC,difA, (float) Diffractometer constants for conversion of d-spacing to TOF
difB in microseconds
-\ Zero (float) Zero point offset (microseconds)
-\ alpha (float) Exponential rise profile coefficients
-\ beta-0 (float) Exponential decay profile coefficients
+\\ Zero (float) Zero point offset (microseconds)
+\\ alpha (float) Exponential rise profile coefficients
+\\ beta-0 (float) Exponential decay profile coefficients
beta-1
beta-q
-\ sig-0 (float) Gaussian profile coefficients
+\\ sig-0 (float) Gaussian profile coefficients
sig-1
sig-2
sig-q
-\ X,Y,Z (float) Lorentzian profile coefficients
+\\ X,Y,Z (float) Lorentzian profile coefficients
Instrument Parameters[1] Pdabc (list of 4 float lists) Originally created for use in gsas as optional tables
of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation
@@ -786,5 +786,5 @@
key sub-key explanation
====================== =============== ====================================================
-Data \ (dict) that contains the
+Data \\ (dict) that contains the
reflection table,
as described in the
@@ -793,5 +793,5 @@
description.
-Instrument Parameters \ (list) containing two dicts where the possible
+Instrument Parameters \\ (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:
@@ -799,11 +799,11 @@
The first and second
values are floats unless otherwise noted.
-\ Lam (two floats) Specifies a wavelength in :math:`\\AA`
-\ Type (two str values) Histogram type :
+\\ Lam (two floats) Specifies a wavelength in :math:`\\AA`
+\\ Type (two str values) Histogram type :
* 'SXC' for constant wavelength x-ray
* 'SNC' for constant wavelength neutron
* 'SNT' for time of flight neutron
-\ InstrName (str) A name for the instrument, used in preparing a CIF
-wtFactor \ (float) A weighting factor to increase or decrease
+\\ InstrName (str) A name for the instrument, used in preparing a CIF
+wtFactor \\ (float) A weighting factor to increase or decrease
the leverage of data in the histogram.
A value of 1.0 weights the data with their
@@ -812,7 +812,7 @@
to decreasing the uncertainties).
-hId \ (int) The number assigned to the histogram when
+hId \\ (int) The number assigned to the histogram when
the project is loaded or edited (can change)
-ranId \ (int) A random number id for the histogram
+ranId \\ (int) A random number id for the histogram
that does not change
====================== =============== ====================================================
@@ -873,5 +873,5 @@
key sub-key explanation
====================== ====================== ====================================================
-Comments \ (list of str) Text strings extracted from the original image data
+Comments \\ (list of str) Text strings extracted from the original image data
header or a metafile. These cannot be changed by
the user; it may be empty.
@@ -881,89 +881,89 @@
X-axis
horizontal.
-\ background image (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted
+\\ 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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.
+\\ 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
+\\ 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.
+\\ 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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) The radiation wavelength (:math:`\\AA`) as entered by the user
+\\ 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) The radiation wavelength (:math:`\\AA`) 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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
+\\ 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.
-\ SpotMask (dict: int & array)
+\\ SpotMask (dict: int & array)
'esdMul'(int) number of standard deviations above mean ring intensity to mask
'spotMask' (bool array) the spot mask for every pixel in image
Stress/Strain Sample phi (float) Sample rotation about vertical axis.
-\ Sample z (float) Sample translation from the calibration sample position (for Sample phi = 0)
+\\ 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
+\\ 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: