Gradient Matrix. Big data boundary misorientation.

Add gradient matrix calculation.
Add small function for progress display.
Add calcBoundaryMisorientation for Big sample, calc misorientation for
grains pairs.

func/OR/close2KOG.m

@@ -1,4 +1,5 @@
 function [a, ind1, ind2, b] = close2KOG(mori, kog, epsilon)
+% Find misorientation close to KOG
 
 b = angle_outer(kog,mori);
 [b,ind] = min(b,[],1);

func/calcBoundaryMisorientationBig.m

@@ -0,0 +1,23 @@
+function [ mori ] = calcBoundaryMisorientationBig( grains, varargin )
+%UNTITLED Summary of this function goes here
+%   Detailed explanation goes here
+
+% Pairs of grains
+[~, pairs] = neighbors(grains);
+
+% One way for getting misorientations and lengths of boundary
+for i = 1:length(pairs)
+    mori0 = calcBoundaryMisorientation(grains(pairs(i,1)),grains(pairs(i,2)), varargin{:});
+    if (i == 1)
+        mori = mori0;
+    else
+        mori = [mori; mori0]; %#ok<AGROW>
+    end
+    if (progressStatus(i,length(pairs),10))
+        fprintf(1,'.');
+    end
+end
+fprintf(1,' - done\n');
+
+end
+

func/dev/progressStatus.m

@@ -0,0 +1,9 @@
+function f = progressStatus( i, n, part )
+%Return true if progress has reached a specified value.
+
+if (mod(i,fix(n/part)) == 0)
+    f = true;
+else
+    f = false;
+end
+

func/misc/gradM.m

@@ -0,0 +1,5 @@
+function L = gradM(R, U)
+
+nabla = R.'/(R*(R.'));
+
+L = (U*nabla).';

tcode/test_FindClosePoints.m

@@ -1,5 +1,6 @@
-ebsd = ak06_load();
-ebsd = cutEBSD(ebsd, 0,0, 100,100);
+%% Load sample
+ebsd = af03s_load();
+ebsd = cutEBSD(ebsd, 50,30, 40,40);
 
 %% Find pattern
 patterns = [];
@@ -14,7 +15,7 @@
     MY = max(Y);
 
     i = randi(length(X),1);
-    a = 1;
+    a = 0.5;
 
     while ((X(i) - mX) <= 2*a || (Y(i) - mY) <= 2*a) || ((MX - X(i)) <= 2*a || (MY - Y(i)) <= 2*a)
         i = randi(length(X),1);
@@ -35,46 +36,77 @@
     X2 = X(ind3);
     Y2 = Y(ind3);
 
-%     scatter(X2,Y2);
-%     axis equal;
     %ind1 - i
     pt = (ind3 - i);
     length(pt)
     patterns(:,k) = pt;
 end
 
+%% Plot pattern
+% scatter(X2,Y2,'fill'); box on;
+% axis equal;
+
 %% Borders
 X1 = X-mX > 1.5*a;
 X2 = MX-X > 1.5*a;
 Y1 = Y-mY > 1.5*a;
 Y2 = MY-Y > 1.5*a;
 
+% Indices of orientation in region
 in_ind = find(X1&X2&Y1&Y2);
 
+% Indices of points and neighbours
 iind2 = repmat(patterns',length(in_ind),1) + repmat(in_ind,1,length(patterns));
 
-scatter(X,Y,5,'sb');
-hold on;
-scatter(X(iind2(:)),Y(iind2(:)),5,'sr');
+% Plot
+% scatter(X,Y,5,'sb');
+% hold on;
+% scatter(X(iind2(:)),Y(iind2(:)),5,'sr');
 
 %% Process all orientation
+% o = get(ebsd,'orientation');
+% c = fix(length(patterns)/2)+1;
+% 
+% for i = 1:length(in_ind)
+%     ind = iind2(i,:);
+%     j = ind(c);
+%     o0 = o(j);
+%     o1 = o(ind);
+%     mo1 = o1\o0;
+%     
+%     dX = X(ind)-X(j);
+%     dY = Y(ind)-Y(j);
+% end
+
+%% Make R and U
+% Get orientations
 o = get(ebsd,'orientation');
+om = o(iind2);
+
+% Center point offset
 c = fix(length(patterns)/2)+1;
 
+% Init matrix
+Rs = zeros(3, length(patterns)*2, length(in_ind));
+Us = zeros(3, length(patterns)*2, length(in_ind));
+
 for i = 1:length(in_ind)
     ind = iind2(i,:);
     j = ind(c);
+
     o0 = o(j);
     o1 = o(ind);
+
     mo1 = o1\o0;
 
-    dX = X(ind)-X(j);
-    dY = Y(ind)-Y(j);
+    U = (angle(mo1)/degree).*vector3d(normalize(axis(mo1)));
+
+    Rs(:,:,i) = [X(ind)' X(ind)'; Y(ind)' Y(ind)'; [-1*ones(1,length(ind)), ones(1,length(ind))];];
+    Us(:,:,i) = [getx(U)' getx(U)'; gety(U)' gety(U)'; getz(U)' getz(U)'];
 end
 
 %% Process all orientation
 
-
 c = mat2cell(o(iind2), ones(1,length(in_ind)), length(pt));
 om = repmat(Eori,length(in_ind),1);