diff --git a/zUtil_Indexter/gtINDEXTER.m b/zUtil_Indexter/gtINDEXTER.m
index a1ddd3ec9179edbad55d27948a393f58a1ce765f..c3a608534ed5d6282234722fe87cafbecbf26f2d 100644
--- a/zUtil_Indexter/gtINDEXTER.m
+++ b/zUtil_Indexter/gtINDEXTER.m
@@ -1,5 +1,11 @@
-function gtINDEXTER(phaseID, flag_update, flag_inputfile, flag_log, forcemerge, parameters)
-% FUNCTION gtINDEXTER(phaseID, flag_update, flag_inputfile, flag_log, forcemerge, parameters)
+function gtINDEXTER(phaseID, flag_update, flag_inputfile, flag_log, ...
+ forcemerge, parameters)
+% GTINDEXTER Grain indexing algorithm Indexter main function.
+%
+% gtINDEXTER(phaseID, flag_update, flag_inputfile, flag_log, ...
+% forcemerge, parameters)
+%
+% --------------------------------------------------------------
%
% Main user function for the Friedel pair indexing algorithm gtIndexter.
% It loads the Friedel pair data from the Spotpair table in the
@@ -388,10 +394,4 @@ fprintf('Total elapsed time: %0.0f sec\n',tEnd)
diary off
-end % of function
-
-
-
-
-
-
+end % of function
\ No newline at end of file
diff --git a/zUtil_Indexter/gtIndexAngularCons.m b/zUtil_Indexter/gtIndexAngularCons.m
index c9341e2dc1c56049f2032834088e7d34d9cd232e..99b87bd14ac988ea61bf3fcf85976abc22178094 100644
--- a/zUtil_Indexter/gtIndexAngularCons.m
+++ b/zUtil_Indexter/gtIndexAngularCons.m
@@ -1,6 +1,6 @@
function uniangles = gtIndexAngularCons(f1,f2,cryst)
%
-% FUNCTION uniangles = gtIndexAngularCons2(f1,f2,cryst)
+% FUNCTION uniangles = gtIndexAngularCons(f1,f2,cryst)
%
% Given two lattice plane families, returns a unique list of
% theoretical angles between plane normals of the two types in real space.
@@ -15,11 +15,11 @@ function uniangles = gtIndexAngularCons(f1,f2,cryst)
% cryst.Bmat
%
% OUTPUT
-% uniangles - unique list of angles in degrees
+% uniangles - unique list of angles in radians
%
% Tolerance for uniqueness in degrees
-TOL = 1e-10;
+TOL = 1e-12;
% Thetatypes (not assuming that they go from 1..n)
th1 = cryst.thetatype(f1);
@@ -42,7 +42,7 @@ n2 = size(v2,1);
angles = zeros(n1*n2,1);
for ii = 1:size(v1,1)
- angles((ii-1)*n2+1:ii*n2) = gtMathsVectorsAngles(v1(ii,:),v2) ;
+ angles((ii-1)*n2+1:ii*n2) = gtMathsVectorsAnglesRad(v1(ii,:), v2, 0) ;
end
% Unique angles with a tolerance
diff --git a/zUtil_Indexter/gtIndexAngularConsMatrix.m b/zUtil_Indexter/gtIndexAngularConsMatrix.m
index 02c051712cccca44498f570af7400c73c108978e..8f010c69331870b3ac6bd166c3c4083af5b355e8 100644
--- a/zUtil_Indexter/gtIndexAngularConsMatrix.m
+++ b/zUtil_Indexter/gtIndexAngularConsMatrix.m
@@ -10,7 +10,7 @@ function ACM = gtIndexAngularConsMatrix(cryst)
% cryst - as in parameters.cryst;
%
% OUTPUT
-% ACM{i,j} - theoretical angles in degrees for any i,j family indices
+% ACM{i,j} - theoretical angles in radians for any i,j family indices
% in cryst; symmetric cell array of size nxn where
% n = length(cryst.thetatype)
%
diff --git a/zUtil_Indexter/gtIndexBuildGrains.m b/zUtil_Indexter/gtIndexBuildGrains.m
index d519eee402fd2c89fa2ac760e4d42c0e46317b32..d22e11d18501711a3f4c1e94839e6044dae7f07a 100644
--- a/zUtil_Indexter/gtIndexBuildGrains.m
+++ b/zUtil_Indexter/gtIndexBuildGrains.m
@@ -1,18 +1,17 @@
-function [grain, unindexed] = gtIndexBuildGrains(remaining_in, tot, ...
- tol_build, cryst, samenv)
-%
-% FUNCTION [grain, unindexed] = gtIndexBuildGrains(remaining_in, tot, ...
-% tol_build, cryst, samenv)
+function [grain, tot] = gtIndexBuildGrains(tot, tol_build, cryst, samenv)
+% GTINDEXBUILDGRAINS Finds new grains (one of the main stages of Indexter).
+%
+% [grain, tot] = gtIndexBuildGrains(tot, tol_build, cryst, samenv)
%
-% 1st/3 Step of the iterative indexing strategy. Finds grains among the
-% reflections, returns the grains with their orientation, position and
+% ----------------------------------------------------------------
+%
+% 1st step out of 3 of the iterative indexing strategy. Finds grains among
+% the reflections, returns the grains with their orientation, position and
% statistical data on the reflections.
-% The signed hkl indices of the reflections are determined.
+% The signed hkl indices of the reflections are also determined.
% Unindexed reflection id-s are returned in 'unindexed'.
%
% INPUT
-%
-% remaining_in - yet unindexed reflection id-s (as in tot.id)
% tot. - all reflection data (including indexed and unindexed)
% tol_build. - tolerances for building grains;
% (as in paramers.index.strategy.b.beg or b.end)
@@ -21,31 +20,29 @@ function [grain, unindexed] = gtIndexBuildGrains(remaining_in, tot, ...
%
% OUTPUT
% grain - grain data (cell vector)
-% unindexed - remaining unindexed reflection id-s
+% tot.indexed - updated; true for the indexed reflection ID-s
%
-
-
+
fprintf('\n BUILDING GRAINS...\n\n')
disp(tol_build)
disp(' ')
tic
-remaining = remaining_in;
nof_grains = 0;
-unindexed = [];
grain = [];
-% Loop until there are reflections left to check
+% Loop through all reflections
-while length(remaining) >= 1
+for ii = 1:length(tot.indexed)
- % Current reflection to be tested
- act = gtIndexSelectRefs(remaining(1), tot);
+ if tot.indexed(ii)
+ continue
+ end
- % Remaining candidate reflections
- cand_rem = gtIndexSelectRefs(remaining(2:end), tot);
+ % Current reflection to be tested
+ act = gtIndexSelectRefsReduced(ii, tot);
% Tolerance for distance between diffraction paths is set equal to the
% approximate grain size times a constant, but is limited to a max.
@@ -53,18 +50,22 @@ while length(remaining) >= 1
tol_build.distf ;
tol_build.dist = min(tol_build.dist, tol_build.distmax) ;
+ % Indices to check
+ inind = ~tot.indexed;
+ inind(1:ii) = false;
+
% Check pair consistency of reflections (all candidates against
% actual).
% 'paircons' is a vector of the linear indices of consistent
- % reflections in cand_rem.
- [paircons, isecs] = gtIndexCheckPairCons(act, cand_rem, ...
- tol_build, samenv, cryst.ACM, tol_build.ming-1);
+ % reflections in tot.
+ [paircons, isecs] = gtIndexCheckPairCons(act, tot, ...
+ tol_build, samenv, cryst.ACM, tol_build.ming-1, inind);
% If there are enough pair consistent candidates
if length(paircons) >= tol_build.ming-1
% Load reflection data for candidates
- cand_paircons = gtIndexSelectRefs([act.id; cand_rem.id(paircons)], tot);
+ cand_paircons = gtIndexSelectRefs([act.id; tot.id(paircons)], tot);
% Find a consistent group among those candidates (check group
% consistency)
@@ -81,24 +82,11 @@ while length(remaining) >= 1
fprintf('Found new grain #%d: %s\n', nof_grains, ...
num2str(grain{nof_grains}.pairid))
- todel = cand_paircons.id(pgroup);
-
- % No consistent group was found for the actual reflection.
- % Put it in unindexed set.
- else
- unindexed = [unindexed; act.id];
- todel = act.id;
+ tot.indexed(cand_paircons.id(pgroup)) = true;
end
- % If there are not enough consistent candidates, put actual reflection
- % in unindexed set
- else
- unindexed = [unindexed; act.id];
- todel = act.id;
end
-
- % Delete reflections which have been dealt with from remaining
- remaining(ismember(remaining,todel)) = [];
+
end
@@ -108,3 +96,4 @@ toc
end % of function
+
diff --git a/zUtil_Indexter/gtIndexCheckAllPairCons.m b/zUtil_Indexter/gtIndexCheckAllPairCons.m
index 640509607a04b592b2d3d80815c3780c1f7ca172..2a65ff003c215b14d427e1177d87e78da6cbc519 100644
--- a/zUtil_Indexter/gtIndexCheckAllPairCons.m
+++ b/zUtil_Indexter/gtIndexCheckAllPairCons.m
@@ -1,7 +1,11 @@
function ok = gtIndexCheckAllPairCons(act, cand, tol, samenv, ACM)
-% FUNCTION ok = gtIndexCheckAllPairCons(act, cand, tol, samenv, ACM)
+% GTINDEXCHECKALLPAIRCONS All positive pair consistency check.
%
-% Checks pair consistency of all reflections in 'cand' against 'act'.
+% ok = gtIndexCheckAllPairCons(act, cand, tol, samenv, ACM)
+%
+% ---------------------------------------------------------
+%
+% Checks whether all reflections in 'cand' are pair consistent with 'act'.
%
% INPUT
% act. - the actual reflection data to be tested against
@@ -60,6 +64,7 @@ end
pofinters = gtMathsLinePairsIntersections([act.ca act.dir],[cand.ca cand.dir]);
cons = gtIndexIsPointInSample(pofinters,samenv);
+
if ~all(cons)
return
end
@@ -68,33 +73,33 @@ end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Check angle
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
% Angles between plane normals consistent?
-cons = false(length(cand.id),1);
-candhklind = cand.hklind;
-candpl = cand.pl;
-actpl = act.pl;
+cons = false(size(cand.pl,1),1);
+
+% Angular tolerance in radians
+tol_ang_rad = tol.ang*pi/180;
% Angular consistency matrix; hklind{} may have more than one element !
ACM_reduced = ACM(act.hklind{1},:);
-% !!! This could be a parfor loop!
-for ii = 1:length(cand.id)
- ACV = ACM_reduced(:,candhklind{ii});
+% Angle between actual and candidates
+ang = gtMathsVectorsAnglesRad(act.pl, cand.pl, 0);
+
+% !!! This could be a parfor loop! But may be too short.
+for ii = 1:size(cand.pl,1)
+ ACV = ACM_reduced(:,cand.hklind{ii});
ACV = vertcat(ACV{:});
-
- ang = gtMathsVectorsAngles(actpl, candpl(ii,:));
- cons(ii) = min(abs(ACV-ang)) < tol.ang;
+ cons(ii) = min(abs(ACV - ang(ii))) < tol_ang_rad;
end
-
if ~all(cons)
return
end
-ok = true;
+% All pairs are consistent
+ok = true;
-end % of function
+end % of function
\ No newline at end of file
diff --git a/zUtil_Indexter/gtIndexCheckPairCons.m b/zUtil_Indexter/gtIndexCheckPairCons.m
index 622d56ac8c5cef3f58cc45245bd9b9edc0b7d509..f6cf064b41e98e5b56f6193fe8587affd8fea40f 100644
--- a/zUtil_Indexter/gtIndexCheckPairCons.m
+++ b/zUtil_Indexter/gtIndexCheckPairCons.m
@@ -1,8 +1,11 @@
function [paircons, pofinters] = gtIndexCheckPairCons(act, cand, tol, ...
- samenv, ACM, minn)
+ samenv, ACM, minn, cons)
+% GTINDEXCHECKPAIRCONS Pair consistency check.
%
-% FUNCTION [paircons, pofinters] = gtIndexCheckPairCons(act, cand, ...
-% tol, samenv, ACM)
+% [paircons, pofinters] = gtIndexCheckPairCons(act, cand, tol, ...
+% samenv, ACM, minn, cons)
+%
+% ---------------------------------------------------------------------
%
% Checks pair consistency of reflection 'act' against a set of others
% in 'cand'.
@@ -14,11 +17,12 @@ function [paircons, pofinters] = gtIndexCheckPairCons(act, cand, tol, ...
% samenv - sample envelope
% ACM - angular consistency matrix
% minn - minimum number of consistent reflections to find
+% cons - candidates to be checked (logical vector)
%
% OUTPUT
% paircons - a vector of logicals; true where 'cand' is pair consistent
-% pofinters - point of 'intersection' between diff. paths of 'act' and
-% consistent 'cand'-s pair wise; empty if found less than
+% pofinters - pair-wise points of 'intersection' between diff. paths of
+% 'act' and the consistent 'cand'-s; empty if found less than
% 'minn' consistent reflections
%
@@ -27,47 +31,27 @@ function [paircons, pofinters] = gtIndexCheckPairCons(act, cand, tol, ...
%% Check bbox sizes and intensity
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% initial indices of consistent reflections
-paircons = (1:length(cand.id))';
-
-
% bbox y size close enough?
-cons = (act.bbys/tol.bbys < cand.bbys) & (cand.bbys < act.bbys*tol.bbys);
-paircons(~cons) = [];
-
-if length(paircons) < minn
- pofinters = [];
- return
-end
-
-
+consm(:,4) = (act.bbys/tol.bbys < cand.bbys) & (cand.bbys < act.bbys*tol.bbys);
% bbox x size close enough?
-cons = (act.bbxs/tol.bbxs < cand.bbxs(paircons)) & (cand.bbxs(paircons) < act.bbxs*tol.bbxs);
-paircons(~cons) = [];
-
-if length(paircons) < minn
- pofinters = [];
- return
-end
-
-
+consm(:,3) = (act.bbxs/tol.bbxs < cand.bbxs) & (cand.bbxs < act.bbxs*tol.bbxs);
% integrated intensities close enough?
-cons = (act.int/tol.int < cand.int(paircons)) & (cand.int(paircons) < act.int*tol.int);
-paircons(~cons) = [];
+consm(:,2) = (act.int/tol.int < cand.int) & (cand.int < act.int*tol.int);
-if length(paircons) < minn
- pofinters = [];
- return
-end
+consm(:,1) = cons;
+cons = all(consm,2);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Check distance and location
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% spatial distance small enough?
-cons = gtMathsLinesDists([act.ca act.dir],[cand.ca(paircons,:) cand.dir(paircons,:)]) < tol.dist ;
-paircons(~cons) = [];
+paircons = find(cons);
+
+% Spatial distance small enough?
+cons2 = gtMathsLinesDists([act.ca act.dir], ...
+ [cand.ca(cons,:) cand.dir(cons,:)]) < tol.dist ;
+paircons(~cons2) = [];
if length(paircons) < minn
pofinters = [];
@@ -85,10 +69,8 @@ pofinters = gtMathsLinePairsIntersections([act.ca act.dir], ...
[cand.ca(paircons,:) cand.dir(paircons,:)]);
cons = gtIndexIsPointInSample(pofinters,samenv);
-
pofinters(~cons,:) = [];
-paircons(~cons) = [];
-
+paircons(~cons) = [];
if length(paircons) < minn
pofinters = [];
@@ -103,24 +85,31 @@ cons = false(length(paircons),1);
candhklind = cand.hklind(paircons);
candpl = cand.pl(paircons,:);
-actpl = act.pl;
-% Angular consistency matrix; hklind{} may have more than one element
-ACM_reduced = ACM(act.hklind{1},:);
+% Angular tolerance in radians
+tol_ang_rad = tol.ang*pi/180;
+
+% Angular consistency matrix for 'act';
+% act.hklind{1} may have more than one element
+ACMact = ACM(act.hklind{1},:);
+
+% Angles between 'act' and 'cand' in radians
+ang = gtMathsVectorsAnglesRad(act.pl, candpl, 0);
% !!! This could be a parfor loop!
for ii = 1:length(paircons)
- ACV = ACM_reduced(:,candhklind{ii});
+ ACV = ACMact(:,candhklind{ii});
ACV = vertcat(ACV{:});
-
- ang = gtMathsVectorsAngles(actpl, candpl(ii,:));
- cons(ii) = min(abs(ACV-ang)) < tol.ang;
+ cons(ii) = min(abs(ACV - ang(ii))) < tol_ang_rad;
end
-
pofinters(~cons,:) = [];
paircons(~cons) = [];
+if length(paircons) < minn
+ pofinters = [];
+end
+
end % of function
diff --git a/zUtil_Indexter/gtIndexExecuteStrategy.m b/zUtil_Indexter/gtIndexExecuteStrategy.m
index 7ad13b49be5926239826d0d3dba0a84d5124a16c..0b48a747c63181038ada49e1f66e3a1ae8b2c2b2 100644
--- a/zUtil_Indexter/gtIndexExecuteStrategy.m
+++ b/zUtil_Indexter/gtIndexExecuteStrategy.m
@@ -1,24 +1,25 @@
function [grain, remaining] = gtIndexExecuteStrategy(strategy, ...
tot, samenv, cryst, grain)
+% GTINDEXEXECUTESTRATEGY Executes the iterative indexing strategy.
%
-% FUNCTION [grain, remaining] = gtIndexExecuteStrategy(strategy, grain, ... tot, samenv, cryst)
-% tot, samenv, cryst)
+% [grain, remaining] = gtIndexExecuteStrategy(strategy, tot, samenv, ...
+% cryst, grain)
+%
+% -----------------------------------------------------------------------
%
% Executes the iterative indexing strategy. Returns the grains that have
% been found and the unindexed reflections.
%
% INPUT
-%
-% strategy. - indexing strategy (as in parameters.index.strategy)
-% tot. - all reflection data (including indexed and unindexed)
-% tol_build. - tolerances for building grains;
-% (as in paramers.index.strategy.b.beg or b.end)
-% cryst. - crystallography and other data
-% samenv. - sample envelope in the Sample reference
+% strategy. - indexing strategy (as in parameters.index.strategy)
+% tot. - all reflection data (including indexed and unindexed)
+% samenv. - sample envelope in the Sample reference
+% cryst. - crystallography and other data
+% grain. - initial grain data
%
% OUTPUT
-% grain - grain data (cell vector)
-% remaining - remaining unindexed reflection id-s
+% grain. - grain data (cell vector)
+% remaining - remaining unindexed reflection id-s
%
@@ -57,13 +58,23 @@ else
strfields = fieldnames(strategy.b.beg);
for ii = 1:length(strfields)
- dif = strategy.b.end.(strfields{ii}) - strategy.b.beg.(strfields{ii});
+ if ((strategy.b.beg.(strfields{ii}) == Inf) || ...
+ (strategy.b.end.(strfields{ii}) == Inf))
+ dif = Inf;
+ else
+ dif = strategy.b.end.(strfields{ii}) - strategy.b.beg.(strfields{ii});
+ end
strategy.l.b.(strfields{ii}) = dif/(strategy.iter-1);
end
strfields = fieldnames(strategy.m.beg);
for ii = 1:length(strfields)
- dif = strategy.m.end.(strfields{ii}) - strategy.m.beg.(strfields{ii});
+ if ((strategy.m.beg.(strfields{ii}) == Inf) || ...
+ (strategy.m.end.(strfields{ii}) == Inf))
+ dif = Inf;
+ else
+ dif = strategy.m.end.(strfields{ii}) - strategy.m.beg.(strfields{ii});
+ end
strategy.l.m.(strfields{ii}) = dif/(strategy.iter-1);
end
@@ -104,12 +115,6 @@ end
nof_refs = length(tot.pairid);
-%grain = [];
-
-% List of all unindexed reflections
-remaining = 1:length(tot.pairid);
-
-
for ii = 1:length(strategy.proc)
fprintf('\n------------ STEP %d/%d ------------\n', ...
@@ -121,7 +126,7 @@ for ii = 1:length(strategy.proc)
% Update the build and merge tolerances.
- fprintf('\n\n LOOSENING TOLERANCES...\n')
+ fprintf('\n LOOSENING TOLERANCES...\n')
strfields = fieldnames(strategy.b.beg);
@@ -143,11 +148,9 @@ for ii = 1:length(strategy.proc)
case 'b' % BUILD GRAINS
% Find new grains among unindexed reflections.
- % grainB - newly created grains
- % remaining - remaining unindexed reflection id-s
-
- [grainB, remaining] = gtIndexBuildGrains(remaining, tot, ...
- tol.b, cryst, samenv);
+ % grainB - newly created grains
+ % tot.indexed - updated
+ [grainB, tot] = gtIndexBuildGrains(tot, tol.b, cryst, samenv);
grain = [grain, grainB];
@@ -155,35 +158,27 @@ for ii = 1:length(strategy.proc)
grain{jj}.id = jj;
end
- cfCheckOutput(grain, remaining, nof_refs)
-
+ cfCheckOutput(grain, sum(~tot.indexed), nof_refs)
case 'm' % MERGE GRAINS
% Find and merge identical grains that have been split.
- % grain - all grain data (will be updated)
-
- if ~isempty(grain)
- [grain, remaining] = gtIndexMergeGrains(grain, remaining, ...
- tot, tol.m, cryst);
- end
+ % grain - all grain data (will be updated)
+ % tot.indexed - updated
+ [grain, tot] = gtIndexMergeGrains(grain, tot, tol.m, cryst);
- cfCheckOutput(grain, remaining, nof_refs)
+ cfCheckOutput(grain, sum(~tot.indexed), nof_refs)
case 'r' % REFINE GRAINS
% Add unindexed reflections to the grains.
- % grain - all grain data (will be updated)
- % remaining - remaining unindexed reflection id-s
+ % grain - all grain data (will be updated)
+ % tot.indexed - updated
+ [grain, tot] = gtIndexRefineGrains(grain, tot, tol.r, cryst);
- if ~isempty(grain)
- [grain, remaining] = gtIndexRefineGrains(grain, ...
- remaining, tot, tol.r, cryst);
- end
-
- cfCheckOutput(grain, remaining, nof_refs)
+ cfCheckOutput(grain, sum(~tot.indexed), nof_refs)
end
@@ -193,6 +188,8 @@ end
fprintf('\n------------ END OF ITERATION ------------\n')
+remaining = find(~tot.indexed);
+
end % of main function
@@ -204,7 +201,7 @@ end % of main function
% Checks if the number of indexed and unindexed reflection is consistent.
-function cfCheckOutput(grain, remaining, nref_orig)
+function cfCheckOutput(grain, nref_remain, nref_orig)
nof_grains = length(grain);
@@ -217,7 +214,7 @@ function cfCheckOutput(grain, remaining, nref_orig)
end
nref_indexed = length(allgrains.pairid);
- nref_remain = length(remaining);
+ %nref_remain = length(remaining);
nref_sum = nref_indexed + nref_remain;
fprintf('\nNumber of ...')
diff --git a/zUtil_Indexter/gtIndexFindGroupInCand.m b/zUtil_Indexter/gtIndexFindGroupInCand.m
index 50c1afeff87bf47c99f68ce08a2900e3780b82a6..6f84bb449da882a098012d11eaa8534e05f8559f 100644
--- a/zUtil_Indexter/gtIndexFindGroupInCand.m
+++ b/zUtil_Indexter/gtIndexFindGroupInCand.m
@@ -1,28 +1,34 @@
function [goods, grain] = gtIndexFindGroupInCand(cand, isecs, tol_build,...
samenv, cryst)
-% This is the function that finds possible new grains in the
-% indexing process.
-% It searches for a possible grain in the input set of candidate
+% GTINDEXFINDGROUPINCAND Core function to find new grains among the
+% reflections
+%
+% [goods, grain] = gtIndexFindGroupInCand(cand, isecs, tol_build,...
+% samenv, cryst)
+%
+% ------------------------------------------------------------------
+%
+% This is the function that finds possible new grains in the
+% indexing process. It searches for a grain in the input set of candidate
% reflections 'cand'.
-% All reflections in 'cand' are pair-consistent with the first reflection
-% in 'cand'. By looping through the rest of the set and checking group-
-% consistency, a 2nd, 3rd, 4th, etc. valid reflection is potentially found.
+% All reflections in 'cand' are assumed to be pair-consistent with the
+% first reflection in 'cand'. By looping through the rest of the set
+% and checking group consistency, a 2nd, 3rd, 4th, etc. valid reflection
+% is potentially found.
%
% INPUT
-%
% cand - reflection data; all the Friedel pairs that possibly belong
% to the same grain as the first one in cand
% isecs - intersection points of the diffraction paths in 3D space;
% size (n,6), where n = length(cand)-1
-% tol_build - indexing tolerances for "building grains"
+% tol_build - indexing tolerances for finding new grains (Build grains)
% samenv - coordinates of the sample envelope
% cryst - crystallography and other data
%
% OUTPUT
-%
% goods - vector of logicals; true for the reflections that
% constitute the new grain; size (n,1)
-% grain - grain data; empty if no valid grain is found
+% grain - grain data; empty if no valid grain was found
%
nof_cand = length(cand.id);
@@ -38,14 +44,14 @@ goods = false(nof_cand,1);
for c1 = 2:nof_cand
% Get data for actual reflection and the following one
- baserefs = gtIndexSelectRefs([1,c1],cand);
+ baserefs = gtIndexSelectRefsReduced([1,c1],cand);
% Loop for finding a 3rd reflection of the grain
for c2 = c1+1:nof_cand
% Check group consistency of this third reflection c2 against the
% other two
- tryref = gtIndexSelectRefs(c2,cand);
+ tryref = gtIndexSelectRefsReduced(c2,cand);
ok = gtIndexCheckGroupCons(tryref, baserefs, isecs(c1-1,:), ...
tol_build, samenv, cryst.ACM);
diff --git a/zUtil_Indexter/gtIndexGrainOutputBasic.m b/zUtil_Indexter/gtIndexGrainOutputBasic.m
index affa8374f284e65d4c091f891c35f51967d76a4e..bed94ec77477c3068fb39395cb422138b24bf1cb 100644
--- a/zUtil_Indexter/gtIndexGrainOutputBasic.m
+++ b/zUtil_Indexter/gtIndexGrainOutputBasic.m
@@ -1,4 +1,10 @@
function [grain, goodind] = gtIndexGrainOutputBasic(grainrefs, cryst, tol_ang)
+% GTINDEXGRAINOUTPUTBASIC Computes basic grain data from a set of
+% reflections.
+%
+% [grain, goodind] = gtIndexGrainOutputBasic(grainrefs, cryst, tol_ang)
+%
+% ---------------------------------------------------------------------
%
% Creates the basic 'grain' data structure from reflections 'grainrefs'.
% Used when a new grain is created or an existing one is modififed.
@@ -11,7 +17,6 @@ function [grain, goodind] = gtIndexGrainOutputBasic(grainrefs, cryst, tol_ang)
% computed.
%
% INPUT
-%
% grainrefs. - grain reflection data
% cryst. - crystallography and other data
% tol_ang - max. angular orientation deviation between two grains
@@ -75,6 +80,10 @@ end
gtCrystRodriguesTestCore(rline, refind, cryst.Rfzone_acc, ...
cryst.Rfzone_ext, tol_Rdist);
+if isempty(Rvec)
+ grain = [];
+ return
+end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Check angular deviation in real space
@@ -122,21 +131,21 @@ dang = acosd(dotprod);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
grain.id = NaN;
-grain.refid = grainrefs.id(goodind)'; % reflection id-s used in indexing
-grain.pairid = grainrefs.pairid(goodind)'; % Friedel pair IDs from matching
+grain.refid = grainrefs.id(goodind)'; % reflection id-s used in indexing
+grain.pairid = grainrefs.pairid(goodind)'; % Friedel pair IDs from matching
grain.R_vector = Rvec; % Rodrigues vector
grain.R_onedge = Ronedge; % Rodrigues vector is close to
% edge of fundamental zone
-grain.nof_pairs = length(goodind); % no. of pairs in grain
+grain.nof_pairs = length(goodind); % no. of pairs in grain
-grain.pl = grainrefs.pl(goodind,:); % plane normals
-grain.hkl = grainrefs.hkl(goodind,:); % hkl families
-grain.theta = grainrefs.theta(goodind); % theta
-grain.int = grainrefs.int(goodind); % intensity
-grain.bbxs = grainrefs.bbxs(goodind); % bbox x size
-grain.bbys = grainrefs.bbys(goodind); % bbox y size
+grain.pl = grainrefs.pl(goodind,:); % plane normals
+grain.hkl = grainrefs.hkl(goodind,:); % hkl families
+grain.theta = grainrefs.theta(goodind); % theta
+grain.int = grainrefs.int(goodind); % intensity
+grain.bbxs = grainrefs.bbxs(goodind); % bbox x size
+grain.bbys = grainrefs.bbys(goodind); % bbox y size
grain.hklind = hklind; % unsigned hkl family linear index
grain.shklind = shklind; % signed hkl linear index
@@ -155,14 +164,8 @@ grain.dcom = gtMathsPointLinesDists(grain.center, ...
grain.indST = zeros(3); % strain tensor in indexing
-%grain.pla = NaN; % theoretical strained plane normal
-%grain.pld = NaN; % theoretical d-spacing
grain.normint = zeros(size(grain.int));
-%grain.difspotidA = [];
-%grain.difspotidB = [];
-
-
% List of shkl-s that have been indexed
grain.shklfound = cryst.shklfound_template; % blank template
@@ -202,9 +205,4 @@ grain.stat.intstd = std(grain.int); % std of intensities
grain.stat.normintstd = std(grain.int); % std of normalised intensities
-
-
-end % of function
-
-
-
+end % of function
\ No newline at end of file
diff --git a/zUtil_Indexter/gtIndexMergeGrains.m b/zUtil_Indexter/gtIndexMergeGrains.m
index d13ec6f35d6c15700d8b3121558c3d8cf30f39fe..ff6d91a8007729dc6c0de1671caad8f51706d05c 100644
--- a/zUtil_Indexter/gtIndexMergeGrains.m
+++ b/zUtil_Indexter/gtIndexMergeGrains.m
@@ -1,17 +1,19 @@
-function [newgrains, unindexed] = gtIndexMergeGrains(grains, ...
- unindexed, tot, tol_merge, cryst)
+function [newgrains, tot] = gtIndexMergeGrains(grains, tot, tol_merge, cryst)
+% GTINDEXMERGEGRAINS Merges grains that seem identical (one of the main
+% stages of Indexter).
%
-% FUNCTION newgrains = gtIndexMergeGrains(grains, tot, tol_merge, cryst)
+% [newgrains, tot] = gtIndexMergeGrains(grains, tot, tol_merge, cryst)
%
-% 2nd/3 Step of the iterative indexing strategy. It looks for
-% combinations of exsiting grains and merges them into one grain if they
+% --------------------------------------------------------------------
+%
+% 2nd of the 3 steps of the iterative indexing strategy. It looks for
+% combinations of existing grains and merges them into one grain if they
% seem to be identical - meaning that the differences in bounding box
% sizes, intensities, location and orientation are within the specified
% tolerances.
-% Grain parameters and statistics for merged grains are updated.
+% Updates grain parameters and statistics for merged grains.
%
% INPUT
-%
% grain - all grain data (cell vector)
% tot. - all reflection data (including indexed and unindexed)
% tol_merge. - tolerances for merging grains;
@@ -20,9 +22,10 @@ function [newgrains, unindexed] = gtIndexMergeGrains(grains, ...
%
% OUTPUT
% grain - updated grain data including merged and unmerged grains
+% tot.indexed - updated; true for reflections indexed in newgrains, false
+% for the rest
%
-
%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Initialize grain data
%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -30,11 +33,17 @@ function [newgrains, unindexed] = gtIndexMergeGrains(grains, ...
fprintf('\n MERGING GRAINS...\n\n')
disp(tol_merge)
disp(' ')
-tic
nof_newgrains = 0;
nof_grains = length(grains);
+if (nof_grains == 0)
+ newgrains = grains;
+ return
+end
+
+tic
+
% Grains indices to be checked
remaining = 1:nof_grains;
@@ -177,7 +186,7 @@ while length(remaining) >= 1
nof_newgrains, num2str(newgrefs.pairid(excind)'))
% Add excluded ones to unindexed set
- unindexed = [unindexed; newgrefs.id(excind)];
+ tot.indexed(newgrefs.id(excind)) = false;
end
@@ -202,9 +211,6 @@ while length(remaining) >= 1
end
-unindexed = sort(unindexed);
-
-
disp(' ')
toc
@@ -212,12 +218,10 @@ toc
end % of main function
-
%%%%%%%%%%%%%%%%%%%%%%%%%%
%% SUB-FUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%
-
function grsel = sfSelectGrains(keeplist,gr)
grsel.id = gr.id(keeplist);
@@ -233,4 +237,3 @@ function grsel = sfSelectGrains(keeplist,gr)
grsel.dang = gr.dang(keeplist);
end
-
diff --git a/zUtil_Indexter/gtIndexRefineGrains.m b/zUtil_Indexter/gtIndexRefineGrains.m
index b3bf6fd952e568077006699ebe0288f7489b5640..e8b3f21856ccb550b7c64824e641968e33c1032b 100644
--- a/zUtil_Indexter/gtIndexRefineGrains.m
+++ b/zUtil_Indexter/gtIndexRefineGrains.m
@@ -1,33 +1,39 @@
-function [grain, remaining] = gtIndexRefineGrains(grain, tryrefids, tot,...
- tol_b, cryst)
+function [grain, tot] = gtIndexRefineGrains(grain, tot, tol_b, cryst)
+% GTINDEXREFINEGRAINS Adds unindexed reflections to grains (one of the
+% main stages of Indexter).
%
-% FUNCTION [grain, remaining] = gtIndexRefineGrains(grain, tryrefids, ...
-% tot, tol_b, cryst)
+% [grain, tot] = gtIndexRefineGrains(grain, tot, tol_b, cryst)
%
-% 3rd/3 Step of the iterative indexing strategy. It loops through all the
-% grains and checks if additional unindexed reflections can be added to
-% them based on tolerances specified for building grains.
+% ------------------------------------------------------------
+%
+% 3rd out of 3 steps of the iterative indexing strategy. It loops through
+% all the grains and checks if additional unindexed reflections can be
+% added to them based on tolerances specified for building grains.
% Grain parameters and statistics for extended grains are updated,
% reflections are checked for multiplicity and least fitting ones are
% rejected if multiplicity exceeds the maximum.
%
% INPUT
-%
% grain. - all grain data (cell vector)
-% tryrefids - unindexed reflection id-s in 'tot' to be tested
% tot. - all reflection data (including indexed and unindexed)
-% tol_merge. - tolerances for building grains;
+% tol_b. - tolerances for building grains;
% (as in paramers.index.strategy.b.beg or b.end)
% cryst. - crystallography and other data
%
% OUTPUT
% grain - updated grain data
-% remaining - remaining unindexed reflection id-s
+% tot.indexed - updated; true for all reflection ID-s indexed in grain,
+% false for the rest
%
fprintf('\n REFINING GRAINS...\n\n')
disp(tol_b)
disp(' ')
+
+if isempty(grain)
+ return
+end
+
tic
% Grains to delete
@@ -54,7 +60,7 @@ for ii = 1:length(grain);
grain{ii}.shkldirs = indshkldirs_cry*cry2sam';
% load data for all candidate reflections
- tryrefs = gtIndexSelectRefs(tryrefids, tot);
+ tryrefs = gtIndexSelectRefs(~tot.indexed, tot);
% check consistency of bbox sizes, intensity, path distance
% and orientation
@@ -66,7 +72,7 @@ for ii = 1:length(grain);
grain{ii}.extended = true;
fprintf('Pairs added to grain #%d : %s\n', ii,...
- num2str(tot.pairid(tryrefids(goodfits))'))
+ num2str(tot.pairid(tryrefs.id(goodfits))'))
end
@@ -74,7 +80,7 @@ for ii = 1:length(grain);
% reflection indices (if grain is found invalid, excrefids contains all
% its refid-s)
[grain{ii}, excrefids] = gtIndexModifyGrain(grain{ii}, [], ...
- tryrefids(goodfits), tot, tol_b, cryst);
+ tryrefs.id(goodfits), tot, tol_b, cryst);
if isempty(grain{ii})
@@ -84,13 +90,11 @@ for ii = 1:length(grain);
% Delete the reflections from list that were added to the grain and add
% back the ones that were rejected:
- tryrefids(goodfits) = [];
- tryrefids = [tryrefids; excrefids];
+ tot.indexed(tryrefs.id(goodfits)) = true;
+ tot.indexed(excrefids) = false;
end
-% Remaining reflections
-remaining = tryrefids;
% Delete bad grains
grain(gtodel) = [];
@@ -99,6 +103,4 @@ grain(gtodel) = [];
disp(' ')
toc
-end
-
-
+end % of function
\ No newline at end of file
diff --git a/zUtil_Indexter/gtIndexSelectRefs.m b/zUtil_Indexter/gtIndexSelectRefs.m
index 4d95dfdc7db6fd8d1b84f51a0c68565104b2e306..8f4219c6a3d4cd6e61550f57f25ef3b823113f33 100644
--- a/zUtil_Indexter/gtIndexSelectRefs.m
+++ b/zUtil_Indexter/gtIndexSelectRefs.m
@@ -1,6 +1,20 @@
function refssel = gtIndexSelectRefs(keeplist, refs)
-% A helper function to load a sub-set 'keeplist' of reflection data from
+% GTINDEXSELECTREFS Helper to load a sub-set of reflections.
+%
+% refssel = gtIndexSelectRefs(keeplist, refs)
+%
+% --------------------------------------------------
+%
+% A helper function to load the sub-set 'keeplist' of reflection data from
% the complete set 'refs'.
+%
+% INPUT
+% keeplist - linear or logical indices of reflections to be selected
+% refs - reflection data
+%
+% OUTPUT
+% refssel - selected sub-set of reflection data
+%
refssel.id = refs.id(keeplist);
diff --git a/zUtil_Indexter/gtIndexSelectRefsReduced.m b/zUtil_Indexter/gtIndexSelectRefsReduced.m
new file mode 100644
index 0000000000000000000000000000000000000000..148b1731aa4075fc321d6705cb9b87a82d07e524
--- /dev/null
+++ b/zUtil_Indexter/gtIndexSelectRefsReduced.m
@@ -0,0 +1,32 @@
+function refssel = gtIndexSelectRefsReduced(keeplist, refs)
+% GTINDEXSELECTREFSREDUCED Helper to load a sub-set of reflections.
+%
+% refssel = gtIndexSelectRefsReduced(keeplist, refs)
+%
+% --------------------------------------------------
+%
+% A helper function to load the sub-set 'keeplist' of reflection data from
+% the complete set 'refs'.
+%
+% INPUT
+% keeplist - linear or logical indices of reflections to be selected
+% refs - reflection data
+%
+% OUTPUT
+% refssel - selected sub-set of reflection data
+%
+
+
+refssel.id = refs.id(keeplist);
+refssel.int = refs.int(keeplist);
+refssel.bbxs = refs.bbxs(keeplist);
+refssel.bbys = refs.bbys(keeplist);
+
+refssel.ca = refs.ca(keeplist,:);
+refssel.dir = refs.dir(keeplist,:);
+refssel.pl = refs.pl(keeplist,:);
+
+refssel.hklind = refs.hklind(keeplist); % cell vector
+
+
+end
\ No newline at end of file
diff --git a/zUtil_Indexter/gtIndexStatisticalFit.m b/zUtil_Indexter/gtIndexStatisticalFit.m
index cd0ca5fa3770643ded8142fe1724e3a6756361aa..d0a54e5541cc28c30a799f05f0c9fd59c6238204 100644
--- a/zUtil_Indexter/gtIndexStatisticalFit.m
+++ b/zUtil_Indexter/gtIndexStatisticalFit.m
@@ -1,28 +1,31 @@
function [grain, remaining] = gtIndexStatisticalFit(grain, restids, tot,...
strategy_s, cryst)
+% GTINDEXSTATISTICALFIT Adds unindexed reflections to grains based on
+% statistics.
+%
+% [grain, remaining] = gtIndexStatisticalFit(grain, restids, ...
+% tot, strategy_s, cryst)
%
-% FUNCTION [grain, remaining] = gtIndexStatisticalFit(grain, restids, ...
-% tot, strategy_s, cryst)
+% ------------------------------------------------------------------
%
-% Adds unindexed reflections to exiting grains based on statistical
-% fitting. those reflections of which intensity, bounding box sizes,
+% Adds unindexed reflections to existing grains based on statistical
+% fitting. Those reflections of which intensity, bounding box sizes,
% distance and angles do not deviate more than the specified tolerance
% value (in std) from the average grain value will be added to the grain.
% If a reflection fits to more than one grain, it will be added to the
% grain it fits best.
%
% INPUT
-% grain - all grain data
-% restids - unindexed reflection id-s
-% tot - all original reflection data
-% strategy_s - parameters for statistical fit
-% (as in parameters.index.strategy.s)
-% cryst - crystallography and other data
+% grain - all grain data
+% restids - unindexed reflection id-s
+% tot - all original reflection data
+% strategy_s - parameters for statistical fit
+% (as in parameters.index.strategy.s)
+% cryst - crystallography and other data
%
% OUTPUT
-% grain - all grain data updated with added reflections
-% remaining - remaining unindedxed reflection id-s after the fit
-%
+% grain - all grain data updated with added reflections
+% remaining - remaining unindedxed reflection ID-s after the fit
%
@@ -120,7 +123,8 @@ remaining(todel) = [];
% Grains to delete
gtodel = [];
-parfor ii = 1:nof_grains
+% !!! ? can be a parfor loop ?
+for ii = 1:nof_grains
if ~isempty(addtograins{ii})
fprintf('Pairs fitted to grain #%d : %s\n', ii, ...
@@ -152,7 +156,6 @@ toc
end % of main function
-
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% SUB-FUNCTIONS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%