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- Nov 2, 2020 12:51:22 PM (3 years ago)
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trunk/GSASIIobj.py (modified) (21 diffs)
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trunk/GSASIIobj.py
r4617 r4638 120 120 key sub-key explanation 121 121 ============= =============== ==================================================== 122 newCellDict \ (dict) ith lattice parameters computed by122 newCellDict \\ (dict) ith lattice parameters computed by 123 123 :func:`GSASIIstrMath.GetNewCellParms` 124 title \ (str) Name of gpx file(?)125 variables \ (list) Values for all N refined variables124 title \\ (str) Name of gpx file(?) 125 variables \\ (list) Values for all N refined variables 126 126 (list of float values, length N, 127 127 ordered to match varyList) 128 sig \ (list) Uncertainty values for all N refined variables128 sig \\ (list) Uncertainty values for all N refined variables 129 129 (list of float values, length N, 130 130 ordered to match varyList) 131 varyList \ (list of str values, length N) List of directly refined variables131 varyList \\ (list of str values, length N) List of directly refined variables 132 132 133 newAtomDict \ (dict) atom position values computed in133 newAtomDict \\ (dict) atom position values computed in 134 134 :func:`GSASIIstrMath.ApplyXYZshifts` 135 Rvals \ (dict) R-factors, GOF, Marquardt value for last135 Rvals \\ (dict) R-factors, GOF, Marquardt value for last 136 136 refinement cycle 137 \ Nobs (int) Number of observed data points138 \ Rwp (float) overall weighted profile R-factor (%)139 \ chisq (float) :math:`\sum w*(I_{obs}-I_{calc})^2`137 \\ Nobs (int) Number of observed data points 138 \\ Rwp (float) overall weighted profile R-factor (%) 139 \\ chisq (float) :math:`\sum w*(I_{obs}-I_{calc})^2` 140 140 for all data. 141 141 Note: this is not the reduced :math:`\chi^2`. 142 \ lamMax (float) Marquardt value applied to Hessian diagonal143 \ GOF (float) The goodness-of-fit, aka square root of142 \\ lamMax (float) Marquardt value applied to Hessian diagonal 143 \\ GOF (float) The goodness-of-fit, aka square root of 144 144 the reduced chi squared. 145 covMatrix \ (np.array) The (NxN) covVariance matrix145 covMatrix \\ (np.array) The (NxN) covVariance matrix 146 146 ============= =============== ==================================================== 147 147 … … 163 163 key sub-key explanation 164 164 ========== =============== ===================================================================================================== 165 General \ (dict) Overall information for the phase166 \ 3Dproj (list of str) projections for 3D pole distribution plots167 \ AngleRadii (list of floats) Default radius for each atom used to compute165 General \\ (dict) Overall information for the phase 166 \\ 3Dproj (list of str) projections for 3D pole distribution plots 167 \\ AngleRadii (list of floats) Default radius for each atom used to compute 168 168 interatomic angles 169 \ AtomMass (list of floats) Masses for atoms170 \ AtomPtrs (list of int) four locations (cx,ct,cs & cu) to use to pull info169 \\ AtomMass (list of floats) Masses for atoms 170 \\ AtomPtrs (list of int) four locations (cx,ct,cs & cu) to use to pull info 171 171 from the atom records 172 \ AtomTypes (llist of str) Atom types173 \ BondRadii (list of floats) Default radius for each atom used to compute172 \\ AtomTypes (llist of str) Atom types 173 \\ BondRadii (list of floats) Default radius for each atom used to compute 174 174 interatomic distances 175 \ Cell Unit cell parameters & ref. flag175 \\ Cell Unit cell parameters & ref. flag 176 176 (list with 8 items. All but first item are float.) 177 177 … … 180 180 4-6: alpha, beta & gamma, (degrees) 181 181 7: volume (:math:`\\AA^3`) 182 \ Color (list of (r,b,g) triplets) Colors for atoms183 \ Compare (dict) Polygon comparison parameters184 \ Data plot type (str) data plot type ('Mustrain', 'Size' or182 \\ Color (list of (r,b,g) triplets) Colors for atoms 183 \\ Compare (dict) Polygon comparison parameters 184 \\ Data plot type (str) data plot type ('Mustrain', 'Size' or 185 185 'Preferred orientation') for powder data 186 \ DisAglCtls (dDict) with distance/angle search controls,186 \\ DisAglCtls (dDict) with distance/angle search controls, 187 187 which has keys 'Name', 'AtomTypes', 188 188 'BondRadii', 'AngleRadii' which are as above … … 191 191 a multiplier for bond and angle search range 192 192 [typically (0.85,0.85)]. 193 \ F000X (float) x-ray F(000) intensity194 \ F000N (float) neutron F(000) intensity195 \ Flip (dict) Charge flip controls196 \ HydIds (dict) geometrically generated hydrogen atoms197 \ Isotope (dict) Isotopes for each atom type198 \ Isotopes (dict) Scattering lengths for each isotope193 \\ F000X (float) x-ray F(000) intensity 194 \\ F000N (float) neutron F(000) intensity 195 \\ Flip (dict) Charge flip controls 196 \\ HydIds (dict) geometrically generated hydrogen atoms 197 \\ Isotope (dict) Isotopes for each atom type 198 \\ Isotopes (dict) Scattering lengths for each isotope 199 199 combination for each element in phase 200 \ MCSA controls (dict) Monte Carlo-Simulated Annealing controls201 \ Map (dict) Map parameters202 \ Mass (float) Mass of unit cell contents in g/mol203 \ Modulated (bool) True if phase modulated204 \ Mydir (str) Directory of current .gpx file205 \ Name (str) Phase name206 \ NoAtoms (dict) Number of atoms per unit cell of each type207 \ POhkl (list) March-Dollase preferred orientation direction208 \ Pawley dmin (float) maximum Q (as d-space) to use for Pawley extraction209 \ Pawley dmax (float) minimum Q (as d-space) to use for Pawley extraction210 \ Pawley neg wt (float) Restraint value for negative Pawley intensities211 \ SGData (object) Space group details as a200 \\ MCSA controls (dict) Monte Carlo-Simulated Annealing controls 201 \\ Map (dict) Map parameters 202 \\ Mass (float) Mass of unit cell contents in g/mol 203 \\ Modulated (bool) True if phase modulated 204 \\ Mydir (str) Directory of current .gpx file 205 \\ Name (str) Phase name 206 \\ NoAtoms (dict) Number of atoms per unit cell of each type 207 \\ POhkl (list) March-Dollase preferred orientation direction 208 \\ Pawley dmin (float) maximum Q (as d-space) to use for Pawley extraction 209 \\ Pawley dmax (float) minimum Q (as d-space) to use for Pawley extraction 210 \\ Pawley neg wt (float) Restraint value for negative Pawley intensities 211 \\ SGData (object) Space group details as a 212 212 :ref:`space group (SGData) <SGData_table>` 213 213 object, as defined in :func:`GSASIIspc.SpcGroup`. 214 \ SH Texture (dict) Spherical harmonic preferred orientation parameters215 \ Super (int) dimension of super group (0,1 only)216 \ Type (str) phase type (e.g. 'nuclear')217 \ Z (dict) Atomic numbers for each atom type218 \ doDysnomia (bool) flag for max ent map modification via Dysnomia219 \ doPawley (bool) Flag for Pawley intensity extraction220 \ vdWRadii (dict) Van der Waals radii for each atom type221 ranId \ (int) unique random number Id for phase222 pId \ (int) Phase Id number for current project.223 Atoms \ (list of lists) Atoms in phase as a list of lists. The outer list214 \\ SH Texture (dict) Spherical harmonic preferred orientation parameters 215 \\ Super (int) dimension of super group (0,1 only) 216 \\ Type (str) phase type (e.g. 'nuclear') 217 \\ Z (dict) Atomic numbers for each atom type 218 \\ doDysnomia (bool) flag for max ent map modification via Dysnomia 219 \\ doPawley (bool) Flag for Pawley intensity extraction 220 \\ vdWRadii (dict) Van der Waals radii for each atom type 221 ranId \\ (int) unique random number Id for phase 222 pId \\ (int) Phase Id number for current project. 223 Atoms \\ (list of lists) Atoms in phase as a list of lists. The outer list 224 224 is for each atom, the inner list contains varying 225 225 items depending on the type of phase, see 226 226 the :ref:`Atom Records <Atoms_table>` description. 227 Drawing \ (dict) Display parameters228 \ Atoms (list of lists) with an entry for each atom that is drawn229 \ Plane (list) Controls for contour density plane display230 \ Quaternion (4 element np.array) Viewing quaternion231 \ Zclip (float) clipping distance in :math:`\\AA`232 \ Zstep (float) Step to de/increase Z-clip233 \ atomPtrs (list) positions of x, type, site sym, ADP flag in Draw Atoms234 \ backColor (list) background for plot as and R,G,B triplet227 Drawing \\ (dict) Display parameters 228 \\ Atoms (list of lists) with an entry for each atom that is drawn 229 \\ Plane (list) Controls for contour density plane display 230 \\ Quaternion (4 element np.array) Viewing quaternion 231 \\ Zclip (float) clipping distance in :math:`\\AA` 232 \\ Zstep (float) Step to de/increase Z-clip 233 \\ atomPtrs (list) positions of x, type, site sym, ADP flag in Draw Atoms 234 \\ backColor (list) background for plot as and R,G,B triplet 235 235 (default = [0, 0, 0], black). 236 \ ballScale (float) Radius of spheres in ball-and-stick display237 \ bondList (dict) Bonds238 \ bondRadius (float) Radius of binds in :math:`\\AA`239 \ cameraPos (float) Viewing position in :math:`\\AA` for plot240 \ contourLevel (float) map contour level in :math:`e/\\AA^3`241 \ contourMax (float) map contour maximum242 \ depthFog (bool) True if use depthFog on plot - set currently as False243 \ ellipseProb (float) Probability limit for display of thermal236 \\ ballScale (float) Radius of spheres in ball-and-stick display 237 \\ bondList (dict) Bonds 238 \\ bondRadius (float) Radius of binds in :math:`\\AA` 239 \\ cameraPos (float) Viewing position in :math:`\\AA` for plot 240 \\ contourLevel (float) map contour level in :math:`e/\\AA^3` 241 \\ contourMax (float) map contour maximum 242 \\ depthFog (bool) True if use depthFog on plot - set currently as False 243 \\ ellipseProb (float) Probability limit for display of thermal 244 244 ellipsoids in % . 245 \ magMult (float) multiplier for magnetic moment arrows246 \ mapSize (float) x & y dimensions of contourmap (fixed internally)247 \ modelView (4,4 array) from openGL drawing transofmation matrix248 \ oldxy (list with two floats) previous view point249 \ radiusFactor (float) Distance ratio for searching for bonds. Bonds245 \\ magMult (float) multiplier for magnetic moment arrows 246 \\ mapSize (float) x & y dimensions of contourmap (fixed internally) 247 \\ modelView (4,4 array) from openGL drawing transofmation matrix 248 \\ oldxy (list with two floats) previous view point 249 \\ radiusFactor (float) Distance ratio for searching for bonds. Bonds 250 250 are located that are within r(Ra+Rb) and (Ra+Rb)/r 251 251 where Ra and Rb are the atomic radii. 252 \ selectedAtoms (list of int values) List of selected atoms253 \ showABC (bool) Flag to show view point triplet. True=show.254 \ showHydrogen (bool) Flag to control plotting of H atoms.255 \ showRigidBodies (bool) Flag to highlight rigid body placement256 \ showSlice (bool) flag to show contour map257 \ sizeH (float) Size ratio for H atoms258 \ unitCellBox (bool) Flag to control display of the unit cell.259 \ vdwScale (float) Multiplier of van der Waals radius for display of vdW spheres.260 \ viewDir (np.array with three floats) cartesian viewing direction261 \ viewPoint (list of lists) First item in list is [x,y,z]252 \\ selectedAtoms (list of int values) List of selected atoms 253 \\ showABC (bool) Flag to show view point triplet. True=show. 254 \\ showHydrogen (bool) Flag to control plotting of H atoms. 255 \\ showRigidBodies (bool) Flag to highlight rigid body placement 256 \\ showSlice (bool) flag to show contour map 257 \\ sizeH (float) Size ratio for H atoms 258 \\ unitCellBox (bool) Flag to control display of the unit cell. 259 \\ vdwScale (float) Multiplier of van der Waals radius for display of vdW spheres. 260 \\ viewDir (np.array with three floats) cartesian viewing direction 261 \\ viewPoint (list of lists) First item in list is [x,y,z] 262 262 in fractional coordinates for the center of 263 263 the plot. Second item list of previous & current 264 264 atom number viewed (may be [0,0]) 265 RBModels \ Rigid body assignments (note Rigid body definitions265 RBModels \\ Rigid body assignments (note Rigid body definitions 266 266 are stored in their own main top-level tree entry.) 267 RMC \ (dict) RMCProfile & rmcfull controls268 Pawley ref \ (list) Pawley reflections269 Histograms \ (dict of dicts) The key for the outer dict is267 RMC \\ (dict) RMCProfile & rmcfull controls 268 Pawley ref \\ (list) Pawley reflections 269 Histograms \\ (dict of dicts) The key for the outer dict is 270 270 the histograms tied to this phase. The inner 271 271 dict contains the combined phase/histogram … … 273 273 size and strain parameters. The following are the 274 274 keys to the inner dict. (dict) 275 \ Babinet (dict) For protein crystallography. Dictionary with two275 \\ Babinet (dict) For protein crystallography. Dictionary with two 276 276 entries, 'BabA', 'BabU' 277 \ Extinction (list of float, bool) Extinction parameter278 \ Flack (list of [float, bool]) Flack parameter & refine flag279 \ HStrain (list of two lists) Hydrostatic strain. The first is277 \\ Extinction (list of float, bool) Extinction parameter 278 \\ Flack (list of [float, bool]) Flack parameter & refine flag 279 \\ HStrain (list of two lists) Hydrostatic strain. The first is 280 280 a list of the HStrain parameters (1, 2, 3, 4, or 6 281 281 depending on unit cell), the second is a list of boolean 282 282 refinement parameters (same length) 283 \ Histogram (str) The name of the associated histogram284 \ Layer Disp (list of [float, bool]) Layer displacement in beam direction & refine flag285 \ LeBail (bool) Flag for LeBail extraction286 \ Mustrain (list) Microstrain parameters, in order:283 \\ Histogram (str) The name of the associated histogram 284 \\ Layer Disp (list of [float, bool]) Layer displacement in beam direction & refine flag 285 \\ LeBail (bool) Flag for LeBail extraction 286 \\ Mustrain (list) Microstrain parameters, in order: 287 287 288 288 0. Type, one of u'isotropic', u'uniaxial', u'generalized' … … 292 292 4. Generalized mustrain parameters - list of 2-6 floats, depending on space group 293 293 5. Generalized refinement flags - list of bools, corresponding to the parameters of (4) 294 \ Pref.Ori. (list) Preferred Orientation. List of eight parameters.294 \\ Pref.Ori. (list) Preferred Orientation. List of eight parameters. 295 295 Items marked SH are only used for Spherical Harmonics. 296 296 … … 303 303 6. (list) SH 304 304 7. (float) SH 305 \ Scale (list of [float, bool]) Phase fraction & refine flag306 \ Size List of crystallite size parameters, in order:305 \\ Scale (list of [float, bool]) Phase fraction & refine flag 306 \\ Size List of crystallite size parameters, in order: 307 307 308 308 0. (str) Type, one of u'isotropic', u'uniaxial', u'ellipsoidal' … … 312 312 4. (list) Ellipsoidal size parameters - list of 6 floats 313 313 5. (list) Ellipsoidal refinement flags - list of bools, corresponding to the parameters of (4) 314 \ Use (bool) True if this histogram is to be used in refinement315 \ newLeBail (bool) Whether to perform a new LeBail extraction316 MCSA \ (dict) Monte-Carlo simulated annealing parameters314 \\ Use (bool) True if this histogram is to be used in refinement 315 \\ newLeBail (bool) Whether to perform a new LeBail extraction 316 MCSA \\ (dict) Monte-Carlo simulated annealing parameters 317 317 ========== =============== ===================================================================================================== 318 318 … … 337 337 ========== =============== ==================================================== 338 338 Vector RBId (dict of dict) vector rigid bodies 339 \ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type340 \ RBname (str) Name assigned by user to rigid body341 \ VectMag (list) vector magnitudes in :math:`\\AA`342 \ rbXYZ (list of 3 float Cartesian coordinates for Vector rigid body )343 \ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin339 \\ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type 340 \\ RBname (str) Name assigned by user to rigid body 341 \\ VectMag (list) vector magnitudes in :math:`\\AA` 342 \\ rbXYZ (list of 3 float Cartesian coordinates for Vector rigid body ) 343 \\ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin 344 344 definition, use center of atoms flag 345 \ VectRef (list of bool refinement flags for VectMag values )346 \ rbTypes (list of str) Atom types for each atom in rigid body347 \ rbVect (list of lists) Cartesian vectors for each translation used to build rigid body348 \ useCount (int) Number of times rigid body is used in any structure345 \\ VectRef (list of bool refinement flags for VectMag values ) 346 \\ rbTypes (list of str) Atom types for each atom in rigid body 347 \\ rbVect (list of lists) Cartesian vectors for each translation used to build rigid body 348 \\ useCount (int) Number of times rigid body is used in any structure 349 349 Residue RBId (dict of dict) residue rigid bodies 350 \ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type351 \ RBname (str) Name assigned by user to rigid body352 \ rbXYZ (list of 3 float) Cartesian coordinates for Residue rigid body353 \ rbTypes (list of str) Atom types for each atom in rigid body354 \ atNames (list of str) Names of each atom in rigid body (e.g. C1,N2...)355 \ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin350 \\ AtInfo (dict) Drad, Color: atom drawing radius & color for each atom type 351 \\ RBname (str) Name assigned by user to rigid body 352 \\ rbXYZ (list of 3 float) Cartesian coordinates for Residue rigid body 353 \\ rbTypes (list of str) Atom types for each atom in rigid body 354 \\ atNames (list of str) Names of each atom in rigid body (e.g. C1,N2...) 355 \\ rbRef (list of 3 int & 1 bool) 3 assigned reference atom nos. in rigid body for origin 356 356 definition, use center of atoms flag 357 \ rbSeq (list) Orig,Piv,angle,Riding : definition of internal rigid body357 \\ rbSeq (list) Orig,Piv,angle,Riding : definition of internal rigid body 358 358 torsion; origin atom (int), pivot atom (int), torsion angle (float), 359 359 riding atoms (list of int) 360 \ SelSeq (int,int) used by SeqSizer to identify objects361 \ useCount (int)Number of times rigid body is used in any structure362 RBIds \ (dict) unique Ids generated upon creation of each rigid body363 \ Vector (list) Ids for each Vector rigid body364 \ Residue (list) Ids for each Residue rigid body360 \\ SelSeq (int,int) used by SeqSizer to identify objects 361 \\ useCount (int)Number of times rigid body is used in any structure 362 RBIds \\ (dict) unique Ids generated upon creation of each rigid body 363 \\ Vector (list) Ids for each Vector rigid body 364 \\ Residue (list) Ids for each Residue rigid body 365 365 ========== =============== ==================================================== 366 366 … … 557 557 key sub-key explanation 558 558 ====================== =============== =========================================================== 559 Comments \ (list of str) Text strings extracted from the original powder559 Comments \\ (list of str) Text strings extracted from the original powder 560 560 data header. These cannot be changed by the user; 561 561 it may be empty. 562 Limits \ (list) two two element lists, as [[Ld,Hd],[L,H]]562 Limits \\ (list) two two element lists, as [[Ld,Hd],[L,H]] 563 563 where L and Ld are the current and default lowest 564 564 two-theta value to be used and 565 565 where H and Hd are the current and default highest 566 566 two-theta value to be used. 567 Reflection Lists \ (dict of dicts) with an entry for each phase in the567 Reflection Lists \\ (dict of dicts) with an entry for each phase in the 568 568 histogram. The contents of each dict item 569 569 is a dict containing reflections, as described in 570 570 the :ref:`Powder Reflections <PowderRefl_table>` 571 571 description. 572 Instrument Parameters \ (dict) The instrument parameters uses different dicts572 Instrument Parameters \\ (dict) The instrument parameters uses different dicts 573 573 for the constant wavelength (CW) and time-of-flight (TOF) 574 574 cases. See below for the descriptions of each. 575 wtFactor \ (float) A weighting factor to increase or decrease575 wtFactor \\ (float) A weighting factor to increase or decrease 576 576 the leverage of data in the histogram . 577 577 A value of 1.0 weights the data with their … … 579 579 increases the weighting of the data (equivalent 580 580 to decreasing the uncertainties). 581 Sample Parameters \ (dict) Parameters that describe how581 Sample Parameters \\ (dict) Parameters that describe how 582 582 the data were collected, as listed 583 583 below. Refinable parameters are a list containing … … 585 585 specifies if the value is refined, otherwise 586 586 the value is a float unless otherwise noted. 587 \ Scale The histogram scale factor (refinable)588 \ Absorption The sample absorption coefficient as587 \\ Scale The histogram scale factor (refinable) 588 \\ Absorption The sample absorption coefficient as 589 589 :math:`\\mu r` where r is the radius 590 590 (refinable). Only valid for Debye-Scherrer geometry. 591 \ SurfaceRoughA Surface roughness parameter A as defined by591 \\ SurfaceRoughA Surface roughness parameter A as defined by 592 592 Surotti, *J. Appl. Cryst*, **5**, 325-331, 1972. 593 593 (refinable - only valid for Bragg-Brentano geometry) 594 \ SurfaceRoughB Surface roughness parameter B (refinable -594 \\ SurfaceRoughB Surface roughness parameter B (refinable - 595 595 only valid for Bragg-Brentano geometry) 596 \ DisplaceX, Sample displacement from goniometer center596 \\ DisplaceX, Sample displacement from goniometer center 597 597 DisplaceY where Y is along the beam direction and 598 598 X is perpendicular. Units are :math:`\\mu m` 599 599 (refinable). 600 \ Phi, Chi, Goniometer sample setting angles, in degrees.600 \\ Phi, Chi, Goniometer sample setting angles, in degrees. 601 601 Omega 602 \ Gonio. radius Radius of the diffractometer in mm603 \ InstrName (str) A name for the instrument, used in preparing602 \\ Gonio. radius Radius of the diffractometer in mm 603 \\ InstrName (str) A name for the instrument, used in preparing 604 604 a CIF . 605 \ Force, Variables that describe how the measurement605 \\ Force, Variables that describe how the measurement 606 606 Temperature, was performed. Not used directly in 607 607 Humidity, any computations. 608 608 Pressure, 609 609 Voltage 610 \ ranId (int) The random-number Id for the histogram610 \\ ranId (int) The random-number Id for the histogram 611 611 (same value as where top-level key is ranId) 612 \ Type (str) Type of diffraction data, may be 'Debye-Scherrer'612 \\ Type (str) Type of diffraction data, may be 'Debye-Scherrer' 613 613 or 'Bragg-Brentano' . 614 hId \ (int) The number assigned to the histogram when614 hId \\ (int) The number assigned to the histogram when 615 615 the project is loaded or edited (can change) 616 ranId \ (int) A random number id for the histogram616 ranId \\ (int) A random number id for the histogram 617 617 that does not change 618 Background \ (list) The background is stored as a list with where618 Background \\ (list) The background is stored as a list with where 619 619 the first item in the list is list and the second 620 620 item is a dict. The list contains the background … … 622 622 Debye diffuse terms and background peaks. 623 623 (TODO: this needs to be expanded.) 624 Data \ (list) The data consist of a list of 6 np.arrays624 Data \\ (list) The data consist of a list of 6 np.arrays 625 625 containing in order: 626 626 … … 658 658 * 'PXC' for constant wavelength x-ray 659 659 * 'PNC' for constant wavelength neutron 660 \ Bank [*] (int) Data set number in a multidata file (usually 1)661 \ Lam (float) Specifies a wavelength in :math:`\\AA`662 \ Lam1 [*] (float) Specifies the primary wavelength in660 \\ Bank [*] (int) Data set number in a multidata file (usually 1) 661 \\ Lam (float) Specifies a wavelength in :math:`\\AA` 662 \\ Lam1 [*] (float) Specifies the primary wavelength in 663 663 :math:`\\AA`, used in place of Lam 664 664 when an :math:`\\alpha_1, \\alpha_2` 665 665 source is used. 666 \ Lam2 [*] (float) Specifies the secondary wavelength in666 \\ Lam2 [*] (float) Specifies the secondary wavelength in 667 667 :math:`\\AA`, used with Lam1 668 \ I(L2)/I(L1) (float) Ratio of Lam2 to Lam1, used with Lam1669 \ Zero (float) Two-theta zero correction in *degrees*670 \ Azimuth [*] (float) Azimuthal setting angle for data recorded with differing setting angles671 \ U, V, W (float) Cagliotti profile coefficients668 \\ I(L2)/I(L1) (float) Ratio of Lam2 to Lam1, used with Lam1 669 \\ Zero (float) Two-theta zero correction in *degrees* 670 \\ Azimuth [*] (float) Azimuthal setting angle for data recorded with differing setting angles 671 \\ U, V, W (float) Cagliotti profile coefficients 672 672 for Gaussian instrumental broadening, where the 673 673 FWHM goes as 674 674 :math:`U \\tan^2\\theta + V \\tan\\theta + W` 675 \ X, Y, Z (float) Cauchy (Lorentzian) instrumental broadening coefficients676 \ SH/L (float) Variant of the Finger-Cox-Jephcoat asymmetric675 \\ X, Y, Z (float) Cauchy (Lorentzian) instrumental broadening coefficients 676 \\ SH/L (float) Variant of the Finger-Cox-Jephcoat asymmetric 677 677 peak broadening ratio. Note that this is the 678 678 sum of S/L and H/L where S is 679 679 sample height, H is the slit height and 680 680 L is the goniometer diameter. 681 \ Polariz. (float) Polarization coefficient.681 \\ Polariz. (float) Polarization coefficient. 682 682 Instrument Parameters[1] (empty dict) 683 683 ======================== =============== =========================================================== … … 707 707 Instrument Parameters[0] Type [*] (str) Histogram type: 708 708 * 'PNT' for time of flight neutron 709 \ Bank (int) Data set number in a multidata file710 \ 2-theta [*] (float) Nominal scattering angle for the detector711 \ fltPath [*] (float) Total flight path source-sample-detector712 \ Azimuth [*] (float) Azimuth angle for detector right hand rotation709 \\ Bank (int) Data set number in a multidata file 710 \\ 2-theta [*] (float) Nominal scattering angle for the detector 711 \\ fltPath [*] (float) Total flight path source-sample-detector 712 \\ Azimuth [*] (float) Azimuth angle for detector right hand rotation 713 713 from horizontal away from source 714 \ difC,difA, (float) Diffractometer constants for conversion of d-spacing to TOF714 \\ difC,difA, (float) Diffractometer constants for conversion of d-spacing to TOF 715 715 difB in microseconds 716 \ Zero (float) Zero point offset (microseconds)717 \ alpha (float) Exponential rise profile coefficients718 \ beta-0 (float) Exponential decay profile coefficients716 \\ Zero (float) Zero point offset (microseconds) 717 \\ alpha (float) Exponential rise profile coefficients 718 \\ beta-0 (float) Exponential decay profile coefficients 719 719 beta-1 720 720 beta-q 721 \ sig-0 (float) Gaussian profile coefficients721 \\ sig-0 (float) Gaussian profile coefficients 722 722 sig-1 723 723 sig-2 724 724 sig-q 725 \ X,Y,Z (float) Lorentzian profile coefficients725 \\ X,Y,Z (float) Lorentzian profile coefficients 726 726 Instrument Parameters[1] Pdabc (list of 4 float lists) Originally created for use in gsas as optional tables 727 727 of d, alp, bet, d-true; for a reflection alpha & beta are obtained via interpolation … … 786 786 key sub-key explanation 787 787 ====================== =============== ==================================================== 788 Data \ (dict) that contains the788 Data \\ (dict) that contains the 789 789 reflection table, 790 790 as described in the … … 793 793 description. 794 794 795 Instrument Parameters \ (list) containing two dicts where the possible795 Instrument Parameters \\ (list) containing two dicts where the possible 796 796 keys in each dict are listed below. The value 797 797 for most items is a list containing two values: … … 799 799 The first and second 800 800 values are floats unless otherwise noted. 801 \ Lam (two floats) Specifies a wavelength in :math:`\\AA`802 \ Type (two str values) Histogram type :801 \\ Lam (two floats) Specifies a wavelength in :math:`\\AA` 802 \\ Type (two str values) Histogram type : 803 803 * 'SXC' for constant wavelength x-ray 804 804 * 'SNC' for constant wavelength neutron 805 805 * 'SNT' for time of flight neutron 806 \ InstrName (str) A name for the instrument, used in preparing a CIF807 wtFactor \ (float) A weighting factor to increase or decrease806 \\ InstrName (str) A name for the instrument, used in preparing a CIF 807 wtFactor \\ (float) A weighting factor to increase or decrease 808 808 the leverage of data in the histogram. 809 809 A value of 1.0 weights the data with their … … 812 812 to decreasing the uncertainties). 813 813 814 hId \ (int) The number assigned to the histogram when814 hId \\ (int) The number assigned to the histogram when 815 815 the project is loaded or edited (can change) 816 ranId \ (int) A random number id for the histogram816 ranId \\ (int) A random number id for the histogram 817 817 that does not change 818 818 ====================== =============== ==================================================== … … 873 873 key sub-key explanation 874 874 ====================== ====================== ==================================================== 875 Comments \ (list of str) Text strings extracted from the original image data875 Comments \\ (list of str) Text strings extracted from the original image data 876 876 header or a metafile. These cannot be changed by 877 877 the user; it may be empty. … … 881 881 X-axis 882 882 horizontal. 883 \ background image (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted883 \\ background image (list:str,float) The name of a tree item ("IMG ...") that is to be subtracted 884 884 during image integration multiplied by value. It must have the same size/shape as 885 885 the integrated image. NB: value < 0 for subtraction. 886 \ calibrant (str) The material used for determining the position/orientation886 \\ calibrant (str) The material used for determining the position/orientation 887 887 of the image. The data is obtained from :func:`ImageCalibrants` 888 888 and UserCalibrants.py (supplied by user). 889 \ calibdmin (float) The minimum d-spacing used during the last calibration run.890 \ calibskip (int) The number of expected diffraction lines skipped during the last889 \\ calibdmin (float) The minimum d-spacing used during the last calibration run. 890 \\ calibskip (int) The number of expected diffraction lines skipped during the last 891 891 calibration run. 892 \ center (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam892 \\ center (list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam 893 893 strikes the detector plane as determined by calibration. This point 894 894 does not have to be within the limits of the detector boundaries. 895 \ centerAzm (bool) If True then the azimuth reported for the integrated slice895 \\ centerAzm (bool) If True then the azimuth reported for the integrated slice 896 896 of the image is at the center line otherwise it is at the leading edge. 897 \ color (str) The name of the colormap used to display the image. Default = 'Paired'.898 \ cutoff (float) The minimum value of I/Ib for a point selected in a diffraction ring for897 \\ color (str) The name of the colormap used to display the image. Default = 'Paired'. 898 \\ cutoff (float) The minimum value of I/Ib for a point selected in a diffraction ring for 899 899 calibration calculations. See pixLimit for details as how point is found. 900 \ DetDepth (float) Coefficient for penetration correction to distance; accounts for diffraction900 \\ DetDepth (float) Coefficient for penetration correction to distance; accounts for diffraction 901 901 ring offset at higher angles. Optionally determined by calibration. 902 \ DetDepthRef (bool) If True then refine DetDepth during calibration/recalibration calculation.903 \ distance (float) The distance (mm) from sample to detector plane.904 \ ellipses (list:lists) Each object in ellipses is a list [center,phi,radii,color] where902 \\ DetDepthRef (bool) If True then refine DetDepth during calibration/recalibration calculation. 903 \\ distance (float) The distance (mm) from sample to detector plane. 904 \\ ellipses (list:lists) Each object in ellipses is a list [center,phi,radii,color] where 905 905 center (list) is location (mm) of the ellipse center on the detector plane, phi is the 906 906 rotation of the ellipse minor axis from the x-axis, and radii are the minor & major 907 907 radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color 908 908 is the selected drawing color (one of 'b', 'g' ,'r') for the ellipse/hyperbola. 909 \ edgemin (float) Not used; parameter in EdgeFinder code.910 \ fullIntegrate (bool) If True then integrate over full 360 deg azimuthal range.911 \ GonioAngles (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image.909 \\ edgemin (float) Not used; parameter in EdgeFinder code. 910 \\ fullIntegrate (bool) If True then integrate over full 360 deg azimuthal range. 911 \\ GonioAngles (list:floats) The 'Omega','Chi','Phi' goniometer angles used for this image. 912 912 Required for texture calculations. 913 \ invert_x (bool) If True display the image with the x-axis inverted.914 \ invert_y (bool) If True display the image with the y-axis inverted.915 \ IOtth (list:floats) The minimum and maximum 2-theta values to be used for integration.916 \ LRazimuth (list:floats) The minimum and maximum azimuth values to be used for integration.917 \ Oblique (list:float,bool) If True apply a detector absorption correction using the value to the913 \\ invert_x (bool) If True display the image with the x-axis inverted. 914 \\ invert_y (bool) If True display the image with the y-axis inverted. 915 \\ IOtth (list:floats) The minimum and maximum 2-theta values to be used for integration. 916 \\ LRazimuth (list:floats) The minimum and maximum azimuth values to be used for integration. 917 \\ Oblique (list:float,bool) If True apply a detector absorption correction using the value to the 918 918 intensities obtained during integration. 919 \ outAzimuths (int) The number of azimuth pie slices.920 \ outChannels (int) The number of 2-theta steps.921 \ pixelSize (list:ints) The X,Y dimensions (microns) of each pixel.922 \ pixLimit (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.919 \\ outAzimuths (int) The number of azimuth pie slices. 920 \\ outChannels (int) The number of 2-theta steps. 921 \\ pixelSize (list:ints) The X,Y dimensions (microns) of each pixel. 922 \\ pixLimit (int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum. 923 923 This value (I) along with the minimum (Ib) in the box is reported by :func:`GSASIIimage.ImageLocalMax` 924 924 and subject to cutoff in :func:`GSASIIimage.makeRing`. 925 925 Locations are used to construct rings of points for calibration calcualtions. 926 \ PolaVal (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from926 \\ PolaVal (list:float,bool) If type='SASD' and if True, apply polarization correction to intensities from 927 927 integration using value. 928 \ rings (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a928 \\ rings (list:lists) Each entry is [X,Y,dsp] where X & Y are lists of x,y coordinates around a 929 929 diffraction ring with the same d-spacing (dsp) 930 \ ring (list) The x,y coordinates of the >5 points on an inner ring930 \\ ring (list) The x,y coordinates of the >5 points on an inner ring 931 931 selected by the user, 932 \ Range (list) The minimum & maximum values of the image933 \ rotation (float) The angle between the x-axis and the vector about which the932 \\ Range (list) The minimum & maximum values of the image 933 \\ rotation (float) The angle between the x-axis and the vector about which the 934 934 detector is tilted. Constrained to -180 to 180 deg. 935 \ SampleShape (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption935 \\ SampleShape (str) Currently only 'Cylinder'. Sample shape for Debye-Scherrer experiments; used for absorption 936 936 calculations. 937 \ SampleAbs (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True937 \\ SampleAbs (list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True 938 938 to cause correction to be applied. 939 \ setDefault (bool) If True the use the image controls values for all new images to be read. (might be removed)940 \ setRings (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.941 \ showLines (bool) If True then isplay the integration limits to be used.942 \ size (list:int) The number of pixels on the image x & y axes943 \ type (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively.944 \ tilt (float) The angle the detector normal makes with the incident beam; range -90 to 90.945 \ wavelength (float) The radiation wavelength (:math:`\\AA`) as entered by the user939 \\ setDefault (bool) If True the use the image controls values for all new images to be read. (might be removed) 940 \\ setRings (bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration. 941 \\ showLines (bool) If True then isplay the integration limits to be used. 942 \\ size (list:int) The number of pixels on the image x & y axes 943 \\ type (str) One of 'PWDR', 'SASD' or 'REFL' for powder, small angle or reflectometry data, respectively. 944 \\ tilt (float) The angle the detector normal makes with the incident beam; range -90 to 90. 945 \\ wavelength (float) The radiation wavelength (:math:`\\AA`) as entered by the user 946 946 (or someday obtained from the image header). 947 947 Masks Arcs (list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask 948 948 to be excluded from integration 949 \ Frames (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside949 \\ Frames (list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside 950 950 of which is excluded from recalibration and integration. Only one frame is allowed. 951 \ Points (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded951 \\ Points (list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded 952 952 from integration. 953 \ Polygons (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image953 \\ Polygons (list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image 954 954 to be excluded from integration. 955 \ Rings (list: lists) Each entry [2-theta,thickness] describes a ring mask955 \\ Rings (list: lists) Each entry [2-theta,thickness] describes a ring mask 956 956 to be excluded from integration. 957 \ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included957 \\ Thresholds (list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included 958 958 in integrsation. The tuple is the image intensity limits and the list are those set by the user. 959 \ SpotMask (dict: int & array)959 \\ SpotMask (dict: int & array) 960 960 'esdMul'(int) number of standard deviations above mean ring intensity to mask 961 961 'spotMask' (bool array) the spot mask for every pixel in image 962 962 963 963 Stress/Strain Sample phi (float) Sample rotation about vertical axis. 964 \ Sample z (float) Sample translation from the calibration sample position (for Sample phi = 0)964 \\ Sample z (float) Sample translation from the calibration sample position (for Sample phi = 0) 965 965 These will be restricted by space group symmetry; result of strain fit refinement. 966 \ Type (str) 'True' or 'Conventional': The strain model used for the calculation.967 \ d-zero (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase966 \\ Type (str) 'True' or 'Conventional': The strain model used for the calculation. 967 \\ d-zero (list:dict) Each item is for a diffraction ring on the image; all items are from the same phase 968 968 and are used to determine the strain tensor. 969 969 The dictionary items are:
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