Mandatory instructions The file must contain the following instructions, which are common for fitallb.py, fitglobalgrain.py and fitgloball.py: NB! Note that the order of the instructions is irrelevant and that extra comments can be added using #, see the example input files.
log_file | name of grainspotter.log from GrainSpotter containing indexing information |
or | |
res_file | name of .gff file from which to read starting grain parameters |
flt_file | name of peaksearch.flt from peaksearch containing filtered peaks information |
par_file | name of detector.par from ImageD11 containing information about experimental setup |
w_step | step size in omega [deg], value in ]0;inf[ |
w_limit | limits of omega intervals [deg], order irrelevant but there must be an even number of limits, values in ]-180;180] |
bg | average background level [counts] on detector, value in ]0;2e16], default: 1000 |
dety_size | detector dimension in y [pixels], default: 2048 (ESRF ID11 Frelon4M) |
detz_size | detector dimension in z [pixels], default: 2048 |
beampol_factor | beam polarisation factor: 1 = fully plane polarised (default), 0 = unpolarised |
beampol_direct | direction of the normal to the plane of the primary beam polarisation with respect to the sample rotation axis [deg] e.g. if the omega rotation axis is parallel to the laboratory z-axis the value is 0.0 (default) and if the rotation is along the y-axis it is 90.0 |
crystal_system | value in {isotropic, cubic, hexagonal, trigonal_high, trigonal_low, tetragonal_high, tetragonal_low, orthorhombic, monoclinic, triclinic} NB! isotropic simply means cubic with isotropic elasticity trigonal_high: 32, 3m, -3m trigonal_low: 3, -3 tetragonal_high: 422, 4mm, -42m, 4/mmm tetragonal_low: 4, -4, 4/m |
title | anything to specify refinement, but remember quotes: 'my very special fitallb farfield refinement title' |
structure_file | name of file containing crystallographic information, possible formats: .cif or .pdf |
sgno | space group number. Onle needed a structure file is not given, and if the grain info is given as a res_file in stead of a log_file |
stress | convert strain to stress (0=no/1=yes), default: 0 |
c11,c12,c44,.. | stiffness constants [Gpa], symmetry given by crystal_system will ensure setup of entire tensor from minimal set, which must be given for stress 1, defaults: None crystal_system required stiffness constants |
isotropic c11,c12 | |
cubic c11,c12,c44 | |
hexagonal c11,c12,c13,c33,c44 | |
trigonal_high c11,c12,c13,c14,c33,c44 | |
trigonal_low c11,c12,c13,c14,c25,c33,c44 | |
tetragonal_high c11,c12,c13,c33,c44,c66 | |
tetragonal_low c11,c12,c13,c16,c33,c44,c66 | |
orthorhombic c11,c12,c13,c22,c23,c33,c44,c55,c66 | |
monoclinic c11,c12,c13,c15,c22,c23,c25,c33,c35,c44,c46,c55,c66 | |
triclinic c11,c12,c13,c14,c15,c16,c22,c23,c24,c25,c26,c33,c34,c35,c36,c44,c45,c46,c55,c56,c66 | |
xyz | fit grain positions (0=no/1=yes), default: 1 |
rod | fit orientations in Rodrigues representation (0=no/1=yes), default: 1 |
eps | fit strain tensors (0=no/1=yes), default: 1 |
tol_grain | tolerance for grain refinement, default: 1e-3 |
rej_ia | outlier rejection limit [deg] for gvector misorientations, value in ]0;inf], default: 0.2 (undeformed material) |
rej_vol | outlier limit for volume/intensity based rejection, value in [3;inf], default: 5 |
rej_resmedian | outlier limit for robust residual based rejection, value in [1;inf], default: 5 |
rej_resmean | outlier rejection limit in terms of average residual, value in [3;inf], default: 10 |
rej_multi | reject peaks assigned to multiple grains (0=no/1=yes), default: 1 |
overlap | fraction of identical peaks assigned to grains before merging is considered, value in ]0;1], default: 1 (no merging) |
min_refl | minimum number of reflections to considered refinement meaningful, value in [1,inf], default: 9 |
skip | skip refinement of the named grains from the grainspotter.log, values in {1,2,...}, default: None |
10 grains of IF steel simulated using PolyXSim within an illuminated volume of 0.7x0.7x0.01 mm with
random orientations, grain sizes and Gaussian strains with a mean of 0 and a spread of 0.001.
The starting values of all grain parameters is read from the if10_near_rotpos.gff generated in the if10 near- and farfield refinement described below to show how resuming a refinement can be done.
Note that the grain positions are kept fixed in this farfield refinement as it can be assumed that the position in if10_near_rotpos.gff are better than what can be refined on a far-field detector.
Runtime approx.~40 sec per grain on a 2.2 GHzm 3.5 GB RAM PC
If near-field refinement of grain position should be performed in fitallb.py, the above far-field options can still be used, but xyz must be 0, near_xyz must be 1 and the following options must be added:
near_flt_file | name of peaksearch.flt filtered peaks file from peaksearch containing near-field data |
near_par_file | name of detector.par file from ImageD11 containing near-field global parameters |
near_bg | average background level [counts] on near-field detector, value in ]0;2e16], default: 100 |
near_dety_size | near-field detector dimension in y [pixels], default: 1536 (ESRF ID11 quantix) |
near_detz_size | near-field detector dimension in z [pixels], default: 1024 |
In addition the following commands may be useful: | |
near_xyz | fit grain positions for near-field data (0=no/1=yes), default: 0 |
near_rod | fit orientations in Rodrigues representation for near-field data (0=no/1=yes), default: 0 |
near_eps | fit strain tensors for near-field data, 0=no only option |
tol_rotpos | tolerance for orientation and position refinement, default: 1e-2 |
near_rej_ia | near-field outlier rejection limits same meaning and defaults as far-field counterparts |
near_rej_vol | |
near_rej_resmedian | |
near_rej_resmean | |
near_rej_multi | |
near_overlap | |
near_min_refl | minimum number of reflections to considered near_field refinement meaningful, value in [1,inf], default: 3 |