# Changeset 1183 for trunk/sphinxdocs/build/html/GSASIIobj.html

Ignore:
Timestamp:
Jan 5, 2014 9:22:22 AM (8 years ago)
Message:

fixup number formatting; update produced doc files

File:
1 edited

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Removed
• ## trunk/sphinxdocs/build/html/GSASIIobj.html

 r1168 (refinable). Only valid for Debye-Scherrer geometry. (refinable).
• Single Crystal Tree Items
• Single Crystal Reflection Data Structure
• Image Data Structure
• Parameter Dictionary
• Classes and routines
• Limits
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]] two-theta value to be used.
Reflection Lists
Reflection Lists A dict with an entry for each phase in the description.
Instrument Parameters
Instrument Parameters A list containing two dicts where the possible Items in the first dict are noted as [1]
Lam Specifies a wavelength in Angstroms [1]
Lam1 Specifies the primary wavelength in source is used [1]

Lam2

I(L2)/I(L1)

Ratio of Lam2 to Lam1 [1]
Type
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 $$U \tan^2\theta + V \tan\theta + W$$ [1]
X, Y Cauchy (Lorentzian) instrumental broadening coefficients [1]
SH/L Variant of the Finger-Cox-Jephcoat asymmetric L is the goniometer diameter. [1]
Polariz. Polarization coefficient. [1]
wtFactor
wtFactor A weighting factor to increase or decrease to decreasing the uncertainties).
Sample Parameters
Sample Parameters Specifies a dict with parameters that describe how the value is a float unless otherwise noted.
Scale The histogram scale factor (refinable)
Absorption The sample absorption coefficient as $$\mu r$$ where r is the radius (refinable).
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, DisplaceY
Phi, Chi, Omega Goniometer sample setting angles, in degrees.
InstrName A name for the instrument, used in preparing a CIF (str).
Force, Temperature, any computations.
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
hId The number assigned to the histogram when the project is loaded or edited (can change)
ranId
ranId A random number id for the histogram that does not change
Background
Background The background is stored as a list with where (TODO: this needs to be expanded.)
Data
Data

The data consist of a list of 6 np.arrays

Image Data StructureÂ¶

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 GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree() and 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.

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 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 GSASIIimage.ImageLocalMax() and subject to cutoff in 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)
strain (list: 3x3 array of float) The strain tensor coefficients [[‘ e11’,’e12’,’e13’],[‘ e21’,’e22’,’e23’],[‘ e31’,’e32’,’e33’]]. 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) d-spacing... ‘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. ‘ImxyCalc’:(list:lists) [[X],[Y]] calculated points based on refined strain.

Parameter DictionaryÂ¶

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 GSASII.GSASII.MakeLSParmDict() and GSASIIIO.ExportBaseclass.loadParmDict()), the values are lists with two elements: [value, refine flag]

When loaded from the GPX file (in GSASIIstrMain.Refine() and 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 routinesÂ¶

This is called in two places (only) GSASIIstrIO.GetUsedHistogramsAndPhases() (which loads the histograms and phases from a GPX file) and GSASII.GSASII.GetUsedHistogramsAndPhases() GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree() (which loads the histograms and phases from the data tree.)

TODO: do we need a lookup for rigid body variables?

Returns:

lbl if not found in labellist or lbl with _1-9 (or `_10-99, etc.) appended at the end

Returns:

lbl if not found in labellist or lbl with _1-9 (or _10-99, etc.) appended at the end

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