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Commit c01f7d5e authored by Peter Reischig's avatar Peter Reischig Committed by Nicola Vigano
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Now input is loaded if not specified. Updated help. 

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@595 4c865b51-4357-4376-afb4-474e03ccb993
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zUtil_Strain2/gtStrainGrainsGeneral.m
+ 70
− 9
View file @ c01f7d5e
......@@ -4,14 +4,43 @@ function [grain, copl, out] = gtStrainGrainsGeneral(grain, cryst, ...
%
% grain = gtStrainGrainsGeneral(grain, cryst, energy, Bmat, errfilt, stdlim)
%
% Runs a strain calculation for all the grains in the cell input 'grain',
% and puts the results in the field grain{i}.strain.
% Runs a strain calculation for all the grains in the cell array 'grain{i}',
% and puts the results in the field 'grain{i}.strain'.
%
% It calls 'gtStrainSingleGrain' to do the strain calculations (see that
% help for more details).
%
% Grains with all coplanar plane normals or with outlier strain values will
% have their strain components set to NaN.
%
% It filters outliers based on their smallest or largest principal strain
% component being away from the median value of all grains more than
% 'stdlim' times the corresponding standard deviation.
%
% OPTIONAL INPUT
% grain - multpile grain data in cell array as output from Indexter
% cryst - crystallography data as in 4_grains/phase_##/index.mat file
% or parameters file
% energy - energy of the X-ray beam in keV
% Bmat - matrix to transform HKL indices into Cartesian coordinates
% errfilt - error filter for pairs (0 < errfilt <= 1); this best fraction
% of Friedel pairs will be used for error fitting;
% e.g. 0.75 meaning the best 75% based on their path distance
% from the grain center of mass; (default is 0.75)
% stdlim - limits in std of all grains' smallest and largest
% principal strain components to reject outlier grains
% (default is Inf)
%
% Either 'grain.hklsp' or 'cryst.shklfam' field is required.
%
% OUTPUT
% grain.strain - new field added containing strain data for each grain
% copl - indices of grains having plane normals that are all
% close to being coplanar
% out - grain indices that have their principal strain components
% identified as outliers
%
%
% Needs the 'cryst' data as in the output of Indexter
% (in file 4_grains/phase_##/index.mat) and the beam energy in keV.
% It filters outliers based on their principal strains being away from the
% median value of all grains more than 'stdlim' times its std.
% The fields 'Bmat' and 'stdlim' are optional.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
......@@ -20,21 +49,53 @@ function [grain, copl, out] = gtStrainGrainsGeneral(grain, cryst, ...
tic
lambda = gtConvEnergyToWavelength(energy);
if ~exist('grain','var') || isempty(grain)
disp('Loading grain info from file 4_grains/phase_01/index.mat.')
index = load('4_grains/phase_01/index.mat');
grain = index.grain;
end
if ~exist('cryst','var') || isempty(cryst)
disp('Loading crystallographic info from file 4_grains/phase_01/index.mat.')
index = load('4_grains/phase_01/index.mat');
cryst = index.cryst;
end
if ~exist('energy','var') || isempty(energy)
disp('Loading beam energy from file parameters.mat.')
parameters = load('parameters.mat');
parameters = parameters.parameters;
energy = parameters.acq.energy;
end
if ~exist('Bmat','var') || isempty(Bmat)
Bmat = gtCrystHKL2CartesianMatrix(cryst.latticepar);
end
if ~exist('errfilt','var') || isempty(errfilt)
errfilt = 0.75;
end
if ~exist('stdlim','var') || isempty(stdlim)
stdlim = Inf;
end
lambda = gtConvEnergyToWavelength(energy);
fprintf('Using the parameters:\n')
fprintf(' Beam energy (keV): %g\n', energy)
fprintf(' Beam wavelength (A): %g\n', lambda)
fprintf(' Error filter: %g%%\n', errfilt*100)
fprintf(' Strain outliers (std): %g\n', stdlim)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Strain fitting
%% Run strain fitting
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
disp('Running strain fitting...')
parfor ii = 1:length(grain)
% Strain fitting (returns 'strain' structure)
......
zUtil_Strain2/gtStrainSingleGrain.m
+ 68
− 37
View file @ c01f7d5e
function strain = gtStrainSingleGrain(grain, cryst, lambda, Bmat, errfilt)
% GTSTRAINSINGLEGRAIN Computes the strain tensor for a single grain.
%
% ST = gtStrainSingleGrain(grain, cryst, lambda, Bmat)
% strain = gtStrainSingleGrain(grain, cryst, lambda, Bmat, errfilt)
%
% Computes the strain tensor 'ST' for a single indexed grain
% Computes the average elastic strain tensor for a single indexed grain
% (crystal system is irrelevant). The 6 strain matrix components are
% computed in the same reference as the plane normals.
% The deformation components are found by fitting all the interplanar
% angles and distances observed (no weighting of the equations).
% computed in the same reference as the plane normals. Small deformations
% are assumed: the strain tensor is the approximated as the symmetric part
% of the deformation gradient tensor. No further approximation is used.
%
% Small deformations are assumed so that the strain tensor is considered to
% be the symmetric part of the deformation tensor, but no further
% approximation is used.
% The best fraction of Friedel pairs (determined by 'errfilt')
% based on their path distance from the center of mass of the grain is
% used for the fitting. Additional pairs are added if needed to avoid all
% plane normals being coplanar. If all plane normals are coplanar,
% there is no strain sensitivity out of that plane, and the results
% are expected to be poor.
%
% It uses the function 'lsqnonlin' from Matlab's Optimization Toolbox.
% The strain components are found by fitting the interplanar angles and
% interplanar distances from the pairs against an undeformed reference
% crystal. Currently there is no weighting of the contribution from the
% different pairs.
%
% The function 'lsqnonlin' from Matlab's Optimization Toolbox is used for
% the fitting.
%
%
% INPUT
% grain - a single grain data as from Indexter
% cryst - crystallography data as in parameters file
% lambda - X-ray beam wavelength
% Bmat - matrix to transform HKL indices into Cartesian coordinates
% (if empty, it will be calculated inside the function)
% grain - a single grain data as from Indexter
% cryst - crystallography data as in index.mat file or parameters file
% lambda - wavelength of the X-ray beam
% Bmat - matrix to transform HKL indices into Cartesian coordinates
% (if empty, it will be calculated inside the function)
% errfilt - error filter for pairs (0 < errfilt <= 1); this best fraction
% of Friedel pairs will be used for error fitting;
% e.g. 0.75 meaning the best 75% based on their path distance
% from the grain center of mass
%
% Either 'grain.hklsp' or 'cryst.shklfam' field is required.
%
% OUTPUT
% ST - strain tensor (approximated as the symmetric part of the
% deformation tensor)
% strain.
% strainT - symmetric small strain tensor
% Eps - strain components in 'strainT' as a vector
% [ST(1,1) ST(2,2) ST(3,3) ST(2,3) ST(1,3) ST(1,2)]
% pstrain - the three principal strain values in descending order
% pstraindir - the three principal directions as column vectors
% corresponding to 'pstrain'
% coplanar - true if the all the plane normals in the grain are close
% to being in the same plane (poor results expected)
% plfitted - true for the plane normals which were used for the
% fitting
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Filter out the worst pairs
%% Parameters to use
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Minimum number of Friedel pairs to be used:
minn = 5;
% Lower limit for the determinant value that estimates how coplanar the
% fitted plane normals are. Should be a value significantly larger than 0.
detlim = 1;
% Initial guess values for fitting the 6 strain components
scguess = [0 0 0 0 0 0];
% Lower and upper bounds for the strain components solution
boundslow = -0.1*ones(1,6);
boundshigh = 0.1*ones(1,6);
% For Matlab's 'lsqnonlin' optimization routine
par.tolx = 1e-6; % precision for components (1e-6 is reasonable and fast)
par.tolfun = 1e-12; % optimization function target value (should be very low)
par.typicalx = 1e-5*ones(1,6); % typical component values for calculating gradients
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Filter out the worst pairs
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plane indices used for strain fitting
plind = false(size(grain.hklind));
......@@ -47,7 +93,7 @@ if (~exist('errfilt','var') || isempty(errfilt) || (errfilt >= 1) || (errfilt <=
% Check that plane normals are not all in one plane (determinant is
% significantly larger than 0 or some tolerance)
detpl = det(pl(:,1:maxind)*pl(:,1:maxind)');
detpl = det(grain.pl*grain.pl');
if (detpl >= detlim)
coplanar = false;
else
......@@ -134,24 +180,9 @@ dotpro_ref(dotpro_ref>1) = 1; % correction for numerical errors
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Optimization
%% Run optimization routine
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initial guess values for fitting the 6 components
scguess = [0 0 0 0 0 0];
% Lower and upper bounds for the components solution
boundslow = -0.1*ones(1,6);
boundshigh = 0.1*ones(1,6);
% Optimization parameters
par.tolx = 1e-6; % precision for components (1e-6 is reasonable and fast)
par.tolfun = 1e-12; % optimization function target value (should be very low)
par.typicalx = 1e-5*ones(1,6); % typical component values for calculating gradients
% Find the "unstrain tensor" components 'sc' that would bring the
% observed, deformed grain into the undeformed reference state. Note that
% rotations have no effect on the interplanar angles or distances,
......@@ -163,9 +194,9 @@ scopt = lsqnonlin( @(sc) sfDeviation(sc, pl, elo_ref, dotpro_ref),...
'TypicalX',par.typicalx, 'FunValCheck','off', 'Display','off'));
%[scopt, resnorm, residual, exitflag, optimout, lagrange, jacobian] = ...
% lsqnonlin( @(sc) sfDeviation(sc, grain.pl, elo_ref, dotpro_ref),...
% lsqnonlin( @(sc) sfDeviation(sc, pl, elo_ref, dotpro_ref),...
% scguess, boundslow, boundshigh,...
% optimset('TolX',par.tolx, 'TolFun',par.tolfun,...
% optimset('TolX',par.tolx, 'TolFun',par.tolfun,...
% 'TypicalX',par.typicalx, 'FunValCheck','off', 'Display','off'));
......@@ -210,7 +241,7 @@ end % of main function
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Sub-function
%% Sub-functions
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Gives a vector of the deviations in interplanar angles and distances
......
0% or .
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