EBSD/Figures: fixes and new map reading function

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

zUtil_Deformation/gtDefCalibrateEBSDMap.m

-function [rot_angle, rot_axis, rot_tensor] = gtDefCalibrateEBSDMap(EBSD_r_map, points, gr, symm)
+function [rot_angle, rot_axis, rot_tensor, rot_vec] = gtDefCalibrateEBSDMap(EBSD_r_map, points, gr, symm)
 
     if (~exist('symm', 'var'))
         symm = gtCrystGetSymmetryOperators();
     end
 
     num_points = numel(gr);
-    for ii = 1:num_points
-%         ref_e_vec = extract_from_map(EBSD_e_map, points{ii});
-%         ref_r_vec = gtMathsEuler2RodInFundZone(ref_e_vec', symm);
-        ref_r_vec = extract_from_map(EBSD_r_map, points{ii});
-        ref_r_vec = gtMathsRod2RodInFundZone(ref_r_vec', symm);
-        % Sometimes the axes definition is not the same
-%         ref_r_vec = [-ref_r_vec(2), ref_r_vec(3), -ref_r_vec(1)];
-
-        gr_r_vec = gr(ii).R_vector;
-        gr_r_vec = gtMathsRod2RodInFundZone(gr_r_vec', symm);
-
-        [rot_vec(ii, :)] = get_angle_axis(ref_r_vec, gr_r_vec, symm); %#ok<AGROW>
-%         [rot_angle(ii), rot_axis(ii, :)] = get_angle_axis(ref_r_vec, gr_r_vec, symm); %#ok<AGROW>
+
+    % Sometimes the axes definition is not the same
+%     ref_r_vec = [-ref_r_vec(2), ref_r_vec(3), -ref_r_vec(1)];
+
+    for ii = num_points:-1:1
+        ref_r_vec(:, ii) = extract_from_map(EBSD_r_map, points{ii});
+        gr_r_vec(:, ii) = gr(ii).R_vector;
     end
 
-%     rot_angle = sum(rot_angle) / num_points;
-%     rot_axis = sum(rot_axis, 1) / num_points;
-%     rot_axis = rot_axis / norm(rot_axis);
+    ref_r_vec = gtMathsRod2RodInFundZone(ref_r_vec, symm);
+    gr_r_vec = gtMathsRod2RodInFundZone(gr_r_vec, symm);
+
+    for ii = num_points:-1:1
+        rot_vec(ii, :) = get_angle_axis(ref_r_vec(:, ii), gr_r_vec(:, ii), symm);
+    end
 
     rot_vec = sum(rot_vec, 1) / num_points;
     rot_angle = 2 * atand(norm(rot_vec));
@@ -33,7 +30,9 @@ function [rot_angle, rot_axis, rot_tensor] = gtDefCalibrateEBSDMap(EBSD_r_map, p
 end
 
 function r_vec_3 = get_angle_axis(r_vec_1, r_vec_2, symm)
-% function [angle, axis] = get_angle_axis(r_vec_1, r_vec_2, symm)
+
+    % gtDisorientation should be used, but it seems to be buggy, at least
+    % for small rotations
 %     [angle, axis] = gtDisorientation(r_vec_1', r_vec_2', symm);
 
     g1 = gtMathsRod2OriMat(r_vec_1);
@@ -43,8 +42,6 @@ function r_vec_3 = get_angle_axis(r_vec_1, r_vec_2, symm)
 
     r_vec_3 = gtMathsOriMat2Rod(M);
     r_vec_3 = gtMathsRod2RodInFundZone(r_vec_3, symm);
-%     angle = 2 * atand(norm(r_vec_3));
-%     axis = r_vec_3 ./ norm(r_vec_3);
 end
 
 function r_vec = extract_from_map(EBSD_r_map, points)

zUtil_Deformation/gtReadEBSDMapIndexingTSVFile.m

+function EBSD_mask = gtReadEBSDMapIndexingTSVFile(filename)
+
+    c = tic();
+    fprintf('Reading from file: "%s"..', filename);
+
+    fid = fopen(filename);
+    % Skipping the first line
+    fgets(fid);
+
+    input = textscan(fid, ['%d' '\t' '%s' ...
+        '\t' '%f' '\t' '%f' '\t' '%f' '\t' '%f' '\t' '%f' '\t' '%f' ...
+        '\t' '%d' '\t' '%d' '\t' '%d' '\t' '%d']);
+    fclose(fid);
+
+    EBSD_mask = cellfun(@(x)strcmpi(x, 'Halite'), input{2});
+
+    fprintf('\b\b, Done in %f seconds.\n', toc(c));
+end
\ No newline at end of file

zUtil_Deformation/plotting/gt6DMakePhaseFigureForPaper.m

@@ -16,6 +16,8 @@ function gt6DMakePhaseFigureForPaper( phase_mat, phase_id, varargin )
 %
 
     conf = struct( ...
+        'lims_u', [], ...
+        'lims_v', [], ...
         'ipf_plane_normal', [], ...
         'use_dmvol', true, ...
         'abs_vol', [], ...
@@ -75,6 +77,20 @@ function gt6DMakePhaseFigureForPaper( phase_mat, phase_id, varargin )
     slice_G(~slice_mask) = slice_abs(~slice_mask);
     slice_B(~slice_mask) = slice_abs(~slice_mask);
 
+    if (~isempty(conf.lims_u))
+        % Note the inversion between x/y because of matlab's transpose problem
+        slice_R = slice_R(conf.lims_u(1):conf.lims_u(2), :, :);
+        slice_G = slice_G(conf.lims_u(1):conf.lims_u(2), :, :);
+        slice_B = slice_B(conf.lims_u(1):conf.lims_u(2), :, :);
+    end
+
+    if (~isempty(conf.lims_v))
+        % Note the inversion between x/y because of matlab's transpose problem
+        slice_R = slice_R(:, conf.lims_v(1):conf.lims_v(2), :);
+        slice_G = slice_G(:, conf.lims_v(1):conf.lims_v(2), :);
+        slice_B = slice_B(:, conf.lims_v(1):conf.lims_v(2), :);
+    end
+
     % Note the inversion between lr/up because of matlab's transpose problem
     if (conf.flip_ud)
         slice_R = fliplr(slice_R);
@@ -87,16 +103,19 @@ function gt6DMakePhaseFigureForPaper( phase_mat, phase_id, varargin )
         slice_B = flipud(slice_B);
     end
 
+    final_slice_RGB = cat(3, slice_R', slice_G', slice_B');
+
     f = figure();
     ax = axes('Parent', f);
-    im = imagesc(cat(3, slice_R', slice_G', slice_B'), 'Parent', ax);
+    im = imagesc(final_slice_RGB, 'Parent', ax);
 
     if (~isempty(conf.clims))
         set(ax, 'CLim', conf.clims)
     end
 
     set(f, 'Units', 'centimeters')
-    img_size = size(slice_ids) * conf.pixel_to_cm;
+    img_size = size(final_slice_RGB) * conf.pixel_to_cm;
+    img_size = img_size([2 1]);
     if (strcmpi(conf.borders, 'no'))
         position = [0, 0, img_size];
         set(f, 'Position', position)

zUtil_Deformation/plotting/gt6DRenderEBSDMapIPF.m

 function gt6DRenderEBSDMapIPF(EBSD_r_map, phase_id, varargin)
 
     conf = struct( ...
+        'mask', [], ...
         'ipf_plane_normal', [], ...
         'flip_ud', false, ...
         'flip_lr', false, ....
         'clims', [], ...
-        'lims_x', [], ...
+        'lims_u', [], ...
+        'lims_v', [], ...
+        'scale', [], ...
         'pixel_to_cm', 0.05, ...
         'borders', 'no', ...
         'colorbar', 'no' );
     conf = parse_pv_pairs(conf, varargin);
 
-    if (~isempty(conf.lims_x))
+    if (~isempty(conf.lims_u))
         % Note the inversion between x/y because of matlab's transpose problem
-        EBSD_r_map = EBSD_r_map(:, conf.lims_x(1):conf.lims_x(2), :);
+        EBSD_r_map = EBSD_r_map(:, conf.lims_u(1):conf.lims_u(2), :);
+    end
+
+    if (~isempty(conf.lims_v))
+        % Note the inversion between x/y because of matlab's transpose problem
+        EBSD_r_map = EBSD_r_map(conf.lims_v(1):conf.lims_v(2), :, :);
+    end
+
+
+    if (~isempty(conf.scale))
+        % Note the inversion between x/y because of matlab's transpose problem
+        EBSD_r_map = imresize(EBSD_r_map, 'nearest', 'scale', conf.scale);
     end
 
     slice_ids = all(EBSD_r_map ~= 0, 3);
@@ -31,6 +45,23 @@ function gt6DRenderEBSDMapIPF(EBSD_r_map, phase_id, varargin)
     slice_G(indx) = cmap(:, 2);
     slice_B(indx) = cmap(:, 3);
 
+    if (~isempty(conf.mask))
+        slice_mask = conf.mask;
+        if (~isempty(conf.lims_u))
+            % Note the inversion between x/y because of matlab's transpose problem
+            slice_mask = slice_mask(:, conf.lims_u(1):conf.lims_u(2), :);
+        end
+
+        if (~isempty(conf.lims_v))
+            % Note the inversion between x/y because of matlab's transpose problem
+            slice_mask = slice_mask(conf.lims_v(1):conf.lims_v(2), :, :);
+        end
+        
+        slice_R(~slice_mask) = 0;
+        slice_G(~slice_mask) = 0;
+        slice_B(~slice_mask) = 0;
+    end
+
     if (conf.flip_lr)
         slice_R = fliplr(slice_R);
         slice_G = fliplr(slice_G);
@@ -47,7 +78,7 @@ function gt6DRenderEBSDMapIPF(EBSD_r_map, phase_id, varargin)
     im = imagesc(cat(3, slice_R, slice_G, slice_B), 'Parent', ax);
 
     set(f, 'Units', 'centimeters')
-    img_size = size(slice_ids) * conf.pixel_to_cm;
+    img_size = size(slice_ids) .* conf.pixel_to_cm;
     img_size = img_size([2 1]);
     if (strcmpi(conf.borders, 'no'))
         position = [0, 0, img_size];