From 99432467dfd650eeaf6b78bd659b7d3057bfad78 Mon Sep 17 00:00:00 2001
From: Nicola Vigano <nicola.vigano@esrf.fr>
Date: Tue, 24 Feb 2015 19:44:14 +0100
Subject: [PATCH] 6D/Visualization: added a bunch of figure-making functions
for generating visual output of the reconstruction
Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>
---
4_grains/gtCalculateGrain.m | 2 +-
.../gt6DCreateProjDataFromGrainCluster.m | 2 +-
zUtil_Deformation/gt6DPlotReconstructionODF.m | 83 +++-----
.../gt6DMakeClusterIPFFigureForPaper.m | 139 +++++++++++++
.../gt6DMakeClusterKAMFigureForPaper.m | 182 ++++++++++++++++++
.../gt6DMakeClusterODFFigureForPaper.m | 143 ++++++++++++++
6 files changed, 494 insertions(+), 57 deletions(-)
create mode 100644 zUtil_Deformation/plotting/gt6DMakeClusterIPFFigureForPaper.m
create mode 100644 zUtil_Deformation/plotting/gt6DMakeClusterKAMFigureForPaper.m
create mode 100644 zUtil_Deformation/plotting/gt6DMakeClusterODFFigureForPaper.m
diff --git a/4_grains/gtCalculateGrain.m b/4_grains/gtCalculateGrain.m
index f15d02ee..53e5c1eb 100644
--- a/4_grains/gtCalculateGrain.m
+++ b/4_grains/gtCalculateGrain.m
@@ -376,6 +376,6 @@ function sfDisplayFigure(parameters, app, grain, det_ind)
hold(ax, 'Off');
- ax_title = sprintf('Fsim for grain %d in phase %d', grain.id, grain.phaseid);
+ ax_title = sprintf('Fsim for grain %d in phase %d', grain.id(1), grain.phaseid);
title(ax, ax_title, 'FontWeight', 'bold');
end
diff --git a/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m b/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
index 2ad8a71a..2b4696df 100644
--- a/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
+++ b/zUtil_Deformation/gt6DCreateProjDataFromGrainCluster.m
@@ -168,7 +168,7 @@ function [refor, estim_space_bbox_pix, estim_orient_bbox] = gt6DCreateProjDataFr
end
refor = struct( ...
- 'id', refgr.id, 'phaseid', refgr.phaseid, ...
+ 'id', refgr.id, 'phaseid', refgr.phaseid, 'gids', grs_list, ...
'center', estim_space_bbox_mm(1:3) + bbox_size_mm / 2, ...
'R_vector', estim_orient_bbox(1:3) + bbox_size_rod / 2 );
refor = gtCalculateGrain(refor, p);
diff --git a/zUtil_Deformation/gt6DPlotReconstructionODF.m b/zUtil_Deformation/gt6DPlotReconstructionODF.m
index 76dbf16b..928bf36f 100644
--- a/zUtil_Deformation/gt6DPlotReconstructionODF.m
+++ b/zUtil_Deformation/gt6DPlotReconstructionODF.m
@@ -1,13 +1,18 @@
-function gt6DPlotReconstructionODF(phase_id, grain_id, percent)
+function gt6DPlotReconstructionODF(phase_id, grain_id, percent, lims_mult)
if (numel(grain_id) > 1)
str_ids = sprintf('_%04d', grain_id);
file_cluster_rec_path = fullfile('4_grains', ...
sprintf('phase_%02d', phase_id), ...
sprintf('grain_cluster_details%s.mat', str_ids));
grain_rec = load(file_cluster_rec_path);
+
+ resolution_multiplier = 1;
else
grain_rec = gtLoadGrainRec(phase_id, grain_id);
+
+ resolution_multiplier = 0.2;
end
+ grain = gtLoadGrain(phase_id, grain_id(1), 'fields', {'R_vector'});
if (~isfield(grain_rec, 'SEG'))
grain_rec.SEG = gtLoadGrain(phase_id, grain_id, ...
@@ -28,7 +33,7 @@ function gt6DPlotReconstructionODF(phase_id, grain_id, percent)
gv_int = int_vol(:);
p = gtLoadParameters();
- resolution = tand(p.labgeo.omstep/2) * 0.2;
+ resolution = tand(p.labgeo.omstep/2) * resolution_multiplier;
grid_points = [ ...
min(grain_rec.ODF6D.R_vectors{1}, [], 1), ...
max(grain_rec.ODF6D.R_vectors{1}, [], 1), ...
@@ -42,48 +47,34 @@ function gt6DPlotReconstructionODF(phase_id, grain_id, percent)
ax2 = subplot(3, 3, 4, 'parent', f);
ax3 = subplot(3, 3, 7, 'parent', f);
- if (false)
- imagesc(sum(odf, 3)', 'parent', ax1);
- imagesc(squeeze(sum(odf, 1))', 'parent', ax2);
- imagesc(squeeze(sum(odf, 2))', 'parent', ax3);
- else
- contourf(sum(odf, 3)', 5, 'parent', ax1)
- contourf(squeeze(sum(odf, 1))', 5, 'parent', ax2)
- contourf(squeeze(sum(odf, 2))', 5, 'parent', ax3)
- end
+ x_pos = 2 * atand(linspace(grid_points(1), grid_points(4), size(odf, 1)) - grain.R_vector(1));
+ y_pos = 2 * atand(linspace(grid_points(2), grid_points(5), size(odf, 2)) - grain.R_vector(2));
+ z_pos = 2 * atand(linspace(grid_points(3), grid_points(6), size(odf, 3)) - grain.R_vector(3));
- x_ticks = linspace(1, size(odf, 1), 5);
- x_tick_labels = 2 * atand(linspace(grid_points(1), grid_points(4), 5) - sum(grid_points([1 4]))/2);
- x_tick_labels = arrayfun(@(x){sprintf('%5.2f', x)}, x_tick_labels);
+ if (~exist('lims_mult', 'var') || isempty(lims_mult))
+ lims_mult = 1;
+ end
- y_ticks = linspace(1, size(odf, 2), 5);
- y_tick_labels = 2 * atand(linspace(grid_points(2), grid_points(5), 5) - sum(grid_points([2 5]))/2);
- y_tick_labels = arrayfun(@(x){sprintf('%5.2f', x)}, y_tick_labels);
+ if (true)
+ imagesc(x_pos, y_pos, sum(odf, 3)', 'parent', ax1);
+ imagesc(y_pos, z_pos, squeeze(sum(odf, 1))', 'parent', ax2);
+ imagesc(x_pos, z_pos, squeeze(sum(odf, 2))', 'parent', ax3);
- z_ticks = linspace(1, size(odf, 3), 5);
- z_tick_labels = 2 * atand(linspace(grid_points(3), grid_points(6), 5) - sum(grid_points([3 6]))/2);
- z_tick_labels = arrayfun(@(x){sprintf('%5.2f', x)}, z_tick_labels);
+ set(ax1, 'CLim', lims_mult * get(ax1, 'CLim'));
+ set(ax2, 'CLim', lims_mult * get(ax2, 'CLim'));
+ set(ax3, 'CLim', lims_mult * get(ax3, 'CLim'));
+ else
+ contourf(x_pos, y_pos, sum(odf, 3)', 5, 'parent', ax1)
+ contourf(y_pos, z_pos, squeeze(sum(odf, 1))', 5, 'parent', ax2)
+ contourf(x_pos, z_pos, squeeze(sum(odf, 2))', 5, 'parent', ax3)
+ end
xlabel(ax1, 'X');
ylabel(ax1, 'Y');
- set(ax1, 'XTick', x_ticks);
- set(ax1, 'XTickLabel', x_tick_labels);
- set(ax1, 'YTick', y_ticks);
- set(ax1, 'YTickLabel', y_tick_labels);
-
xlabel(ax2, 'Y');
ylabel(ax2, 'Z');
- set(ax2, 'XTick', y_ticks);
- set(ax2, 'XTickLabel', y_tick_labels);
- set(ax2, 'YTick', z_ticks);
- set(ax2, 'YTickLabel', z_tick_labels);
-
xlabel(ax3, 'X');
ylabel(ax3, 'Z');
- set(ax3, 'XTick', x_ticks);
- set(ax3, 'XTickLabel', x_tick_labels);
- set(ax3, 'YTick', z_ticks);
- set(ax3, 'YTickLabel', z_tick_labels);
colormap(ax1, gray);
colormap(ax2, gray);
@@ -93,37 +84,19 @@ function gt6DPlotReconstructionODF(phase_id, grain_id, percent)
if (~exist('percent', 'var') || isempty(percent))
percent = 0.2;
end
- thr_value = (max(odf(:)) - min(odf(:))) * percent + min(odf(:));
- p = patch(isosurface(permute(odf, [2 1 3]), thr_value), 'parent', ax4);
+ thr_value = (max(odf(:)) - min(odf(:))) * percent * lims_mult + min(odf(:));
+ p = patch(isosurface(x_pos, y_pos, z_pos, permute(odf, [2 1 3]), thr_value), 'parent', ax4);
set(p, 'FaceColor', 'cyan', 'EdgeColor', 'none')
axis(ax4, 'tight')
camlight('right')
camlight('left')
lighting('gouraud')
-
- x_ticks = linspace(1, size(odf, 1), 15);
- x_tick_labels = 2 * atand(linspace(grid_points(1), grid_points(4), 15) - sum(grid_points([1 4]))/2);
- x_tick_labels = arrayfun(@(x){sprintf('%5.2f', x)}, x_tick_labels);
-
- y_ticks = linspace(1, size(odf, 2), 15);
- y_tick_labels = 2 * atand(linspace(grid_points(2), grid_points(5), 15) - sum(grid_points([2 5]))/2);
- y_tick_labels = arrayfun(@(x){sprintf('%5.2f', x)}, y_tick_labels);
-
- z_ticks = linspace(1, size(odf, 3), 15);
- z_tick_labels = 2 * atand(linspace(grid_points(3), grid_points(6), 15) - sum(grid_points([3 6]))/2);
- z_tick_labels = arrayfun(@(x){sprintf('%5.2f', x)}, z_tick_labels);
+ grid(ax4, 'on')
xlabel(ax4, 'X');
ylabel(ax4, 'Y');
zlabel(ax4, 'Z');
- set(ax4, 'XTick', x_ticks);
- set(ax4, 'XTickLabel', x_tick_labels);
- set(ax4, 'YTick', y_ticks);
- set(ax4, 'YTickLabel', y_tick_labels);
- set(ax4, 'ZTick', z_ticks);
- set(ax4, 'ZTickLabel', z_tick_labels);
-
set(f, 'Units', 'centimeters')
pos = get(f, 'Position');
pos(3:4) = pos(3:4) * 1.5;
diff --git a/zUtil_Deformation/plotting/gt6DMakeClusterIPFFigureForPaper.m b/zUtil_Deformation/plotting/gt6DMakeClusterIPFFigureForPaper.m
new file mode 100644
index 00000000..ac5168c7
--- /dev/null
+++ b/zUtil_Deformation/plotting/gt6DMakeClusterIPFFigureForPaper.m
@@ -0,0 +1,139 @@
+function gt6DMakeClusterIPFFigureForPaper(cluster, cluster_rec, varargin)
+% function gt6DMakeClusterIPFFigureForPaper(cluster, cluster_rec, varargin)
+
+ conf = struct( ...
+ 'plane_normal', [0 0 1], ...
+ 'kam_bound', 0.2, ...
+ 'filename', '', ...
+ 'plane', 'xy', ...
+ 'flip_ud', false, ...
+ 'flip_lr', false, ...
+ 'slice', 1, ...
+ 'clims', [0 1], ...
+ 'show_labels', false, ...
+ 'pixel_to_cm', 0.1, ...
+ 'borders', 'no', ...
+ 'colorbar', 'no' );
+ conf = parse_pv_pairs(conf, varargin);
+
+ if (~exist('cluster_rec', 'var') || isempty(cluster_rec))
+ cluster_rec = gtLoadClusterRec(cluster.phaseid, cluster.gids);
+ end
+
+ internal_shift = cluster_rec.SEG.segbb(1:3) - cluster_rec.ODF6D.shift + 1;
+ seg_vol_bb = [internal_shift, cluster_rec.SEG.segbb(4:6)];
+
+ seg_vol = logical(cluster_rec.SEG.seg);
+
+ dm_vol(:, :, :, 3) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 3), seg_vol_bb) .* seg_vol;
+ dm_vol(:, :, :, 2) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 2), seg_vol_bb) .* seg_vol;
+ dm_vol(:, :, :, 1) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 1), seg_vol_bb) .* seg_vol;
+
+ slice_rod = get_slice(dm_vol, conf.plane, conf.slice);
+ slice_seg = get_slice(seg_vol, conf.plane, conf.slice);
+ r_vecs = reshape(slice_rod, [], 3);
+ r_vecs = r_vecs(slice_seg(:), :);
+
+ [cmap, ~, ~] = gtIPFCmap(cluster.phaseid, conf.plane_normal, ...
+ 'r_vectors', r_vecs, 'background', false);
+
+ slice_R = zeros(size(slice_seg));
+ slice_G = zeros(size(slice_seg));
+ slice_B = zeros(size(slice_seg));
+
+ slice_R(slice_seg(:)) = cmap(:, 1);
+ slice_G(slice_seg(:)) = cmap(:, 2);
+ slice_B(slice_seg(:)) = cmap(:, 3);
+
+ int_vol = gtCrop(cluster_rec.ODF6D.intensity, seg_vol_bb) .* seg_vol;
+ slice_int_vol = get_slice(int_vol, conf.plane, conf.slice, true);
+ slice_dm_vol = get_slice(dm_vol, conf.plane, conf.slice, true);
+
+ % needed for the high anglular boundaries
+ [slice_kam, slice_gam] = gtDefComputeKernelAverageMisorientation(slice_dm_vol, slice_int_vol);
+ slice_kam = squeeze(slice_kam);
+ high_ang = slice_kam > conf.kam_bound;
+
+ slice_R(high_ang) = 0;
+ slice_G(high_ang) = 0;
+ slice_B(high_ang) = 0;
+
+ %
+
+ % Note the inversion between lr/up because of matlab's transpose problem
+ if (conf.flip_ud)
+ slice_R = fliplr(slice_R);
+ slice_G = fliplr(slice_G);
+ slice_B = fliplr(slice_B);
+
+ slice_seg = fliplr(slice_seg);
+ end
+ if (conf.flip_lr)
+ slice_R = flipud(slice_R);
+ slice_G = flipud(slice_G);
+ slice_B = flipud(slice_B);
+
+ slice_seg = flipud(slice_seg);
+ end
+
+ f = figure();
+ ax = axes('parent', f);
+ imagesc(cat(3, slice_R', slice_G', slice_B'), 'parent', ax, ...
+ 'AlphaDataMapping', 'scaled', 'AlphaData', slice_seg' );
+ colormap(ax, jet)
+
+ set_size(f, ax, conf, slice_kam);
+
+ drawnow();
+end
+
+function slice = get_slice(vol, plane, slice_idx, no_squeeze)
+ switch(plane)
+ case {'xy', 'XY'}
+ slice = vol(:, :, slice_idx, :);
+ case {'yx', 'YX'}
+ slice = permute(vol(:, :, slice_idx, :), [2 1 3 4]);
+ case {'yz', 'YZ'}
+ slice = vol(slice_idx, :, :, :);
+ case {'zy', 'ZY'}
+ slice = permute(vol(slice_idx, :, :, :), [1 3 2 4]);
+ case {'xz', 'XZ'}
+ slice = vol(:, slice_idx, :, :);
+ case {'zx', 'ZX'}
+ slice = permute(vol(:, slice_idx, :, :), [3 2 1 4]);
+ end
+ if (~exist('no_squeeze', 'var') || isempty(no_squeeze) || ~no_squeeze)
+ slice = squeeze(slice);
+ end
+end
+
+function set_size(f, ax, conf, slice_kam)
+ set(f, 'Units', 'centimeters')
+ img_size = size(slice_kam) * conf.pixel_to_cm;
+ if (strcmpi(conf.borders, 'no'))
+ position = [0, 0, img_size];
+ set(f, 'Position', position)
+ set(f, 'Paperposition', position)
+
+ set(ax, 'Units', 'normalized')
+ set(ax, 'Position', [0, 0, 1, 1])
+ else
+ set(ax, 'Units', 'centimeters')
+ if (strcmpi(conf.colorbar, 'no'))
+ position = [0, 0, img_size] + [0, 0, 2, 1.5];
+ set(f, 'Position', position)
+ set(f, 'Paperposition', position)
+ else
+ position = [0, 0, img_size] + [0, 0, 3, 1.5];
+ set(f, 'Position', position)
+ set(f, 'Paperposition', position)
+
+ cb = colorbar('peer', ax, 'location', 'EastOutside');
+ set(cb, 'Units', 'centimeters')
+ position = [img_size(1)+1.35, 1, 0.65, img_size(2)];
+ set(cb, 'Position', position)
+ end
+ position = [1, 1, img_size];
+ set(ax, 'Position', position)
+ end
+end
diff --git a/zUtil_Deformation/plotting/gt6DMakeClusterKAMFigureForPaper.m b/zUtil_Deformation/plotting/gt6DMakeClusterKAMFigureForPaper.m
new file mode 100644
index 00000000..bb684147
--- /dev/null
+++ b/zUtil_Deformation/plotting/gt6DMakeClusterKAMFigureForPaper.m
@@ -0,0 +1,182 @@
+function gt6DMakeClusterKAMFigureForPaper(cluster, cluster_rec, grs, varargin)
+% function gt6DMakeClusterKAMFigureForPaper(cluster, cluster_rec, grs, varargin)
+
+ conf = struct( ...
+ 'percent', 0.0025, ...
+ 'filename', '', ...
+ 'plane', 'xy', ...
+ 'flip_ud', false, ...
+ 'flip_lr', false, ...
+ 'slice', 1, ...
+ 'clims', [0 1], ...
+ 'show_labels', false, ...
+ 'pixel_to_cm', 0.1, ...
+ 'borders', 'yes', ...
+ 'colorbar', 'yes' );
+ conf = parse_pv_pairs(conf, varargin);
+
+ if (~exist('cluster_rec', 'var') || isempty(cluster_rec))
+ cluster_rec = gtLoadClusterRec(cluster.phaseid, cluster.gids);
+ end
+ if (~exist('grs', 'var') || isempty(grs))
+ grs = gtLoadGrain(cluster.phaseid, cluster.gids);
+ end
+
+ internal_shift = cluster_rec.SEG.segbb(1:3) - cluster_rec.ODF6D.shift + 1;
+ seg_vol_bb = [internal_shift, cluster_rec.SEG.segbb(4:6)];
+
+ seg_vol = logical(cluster_rec.SEG.seg);
+
+ dm_vol(:, :, :, 3) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 3), seg_vol_bb) .* seg_vol;
+ dm_vol(:, :, :, 2) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 2), seg_vol_bb) .* seg_vol;
+ dm_vol(:, :, :, 1) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 1), seg_vol_bb) .* seg_vol;
+
+ int_vol = gtCrop(cluster_rec.ODF6D.intensity, seg_vol_bb) .* seg_vol;
+
+ [kam, gam] = gtDefComputeKernelAverageMisorientation(dm_vol, int_vol);
+ gam
+ [igm, gos] = gtDefComputeIntraGranularMisorientation(dm_vol, int_vol, 'R_vector', grs(1).R_vector);
+ gos
+
+ slice_kam = get_slice(kam, conf.plane, conf.slice);
+ slice_igm = get_slice(igm, conf.plane, conf.slice);
+ slice_seg = get_slice(seg_vol, conf.plane, conf.slice);
+
+ %
+
+ % Note the inversion between lr/up because of matlab's transpose problem
+ if (conf.flip_ud)
+ slice_kam = fliplr(slice_kam);
+ slice_igm = fliplr(slice_igm);
+ slice_seg = fliplr(slice_seg);
+ end
+ if (conf.flip_lr)
+ slice_kam = flipud(slice_kam);
+ slice_igm = flipud(slice_igm);
+ slice_seg = flipud(slice_seg);
+ end
+
+ clims_kam = [conf.clims(1), min(conf.clims(2), max(slice_kam(:)))];
+
+ f = figure();
+ ax = axes('parent', f);
+ imagesc(slice_kam', 'parent', ax, ...
+ 'AlphaDataMapping', 'scaled', 'AlphaData', slice_seg', ...
+ clims_kam );
+ colormap(ax, jet)
+
+ if (conf.show_labels)
+ t = uicontrol('Style', 'Text', 'parent', f, ...
+ 'String', sprintf('Grain Average Misorientation: %.3g°', gam), ...
+ 'FontWeight', 'bold');
+
+ set_size(f, ax, t, conf, slice_kam);
+ else
+ set_size(f, ax, [], conf, slice_kam);
+ end
+
+ drawnow();
+
+ clims_igm = [conf.clims(1), max(slice_igm(:))];
+
+ f = figure();
+ ax = axes('parent', f);
+ imagesc(slice_igm', 'parent', ax, ...
+ 'AlphaDataMapping', 'scaled', 'AlphaData', slice_seg', ...
+ clims_igm );
+ colormap(ax, jet);
+
+ if (conf.show_labels)
+ t = uicontrol('Style', 'Text', 'parent', f, ...
+ 'String', sprintf('Grain Orientation Spread: %.3g°', gos), ...
+ 'FontWeight', 'bold');
+
+ set_size(f, ax, t, conf, slice_kam);
+ else
+ set_size(f, ax, [], conf, slice_kam);
+ end
+
+ drawnow();
+
+ %
+
+% if (~isempty(conf.filename) && strcmpi(conf.filename, 'preview'))
+% [filename, filedir] = uigetfile({'*.png'; '*.eps'});
+% if (filename)
+% conf.filename = fullfile(filedir, filename);
+% else
+% conf.filename = [];
+% end
+% end
+%
+% if (~isempty(conf.filename))
+% [~, ~, ext] = fileparts(conf.filename);
+% if (isempty(ext))
+% saveas(f, [conf.filename '.eps']);
+% saveas(f, [conf.filename '.png']);
+% else
+% saveas(f, conf.filename);
+% end
+% end
+end
+
+function slice = get_slice(vol, plane, slice_idx)
+ switch(plane)
+ case {'xy', 'XY'}
+ slice = vol(:, :, slice_idx, :);
+ case {'yx', 'YX'}
+ slice = permute(vol(:, :, slice_idx, :), [2 1 3]);
+ case {'yz', 'YZ'}
+ slice = squeeze(vol(slice_idx, :, :, :));
+ case {'zy', 'ZY'}
+ slice = permute(squeeze(vol(slice_idx, :, :, :)), [2 1 3]);
+ case {'xz', 'XZ'}
+ slice = squeeze(vol(:, slice_idx, :, :));
+ case {'zx', 'ZX'}
+ slice = permute(squeeze(vol(:, slice_idx, :, :)), [2 1 3]);
+ end
+end
+
+function set_size(f, ax, t, conf, slice_kam)
+ set(f, 'Units', 'centimeters')
+ img_size = size(slice_kam) * conf.pixel_to_cm;
+ if (strcmpi(conf.borders, 'no'))
+ position = [0, 0, img_size];
+ set(f, 'Position', position)
+ set(f, 'Paperposition', position)
+
+ set(ax, 'Units', 'normalized')
+ set(ax, 'Position', [0, 0, 1, 1])
+ else
+ if (conf.show_labels)
+ upper_padding = 2;
+ lower_offset = 1.75;
+ else
+ upper_padding = 1.5;
+ lower_offset = 1;
+ end
+ set(ax, 'Units', 'centimeters')
+ if (strcmpi(conf.colorbar, 'no'))
+ position = [0, 0, img_size] + [0, 0, 2, upper_padding];
+ set(f, 'Position', position)
+ set(f, 'Paperposition', position)
+ else
+ position = [0, 0, img_size] + [0, 0, 3, upper_padding];
+ set(f, 'Position', position)
+ set(f, 'Paperposition', position)
+
+ cb = colorbar('peer', ax, 'location', 'EastOutside');
+ set(cb, 'Units', 'centimeters')
+ position = [img_size(1)+1.35, lower_offset, 0.65, img_size(2)];
+ set(cb, 'Position', position)
+ end
+ position = [1, lower_offset, img_size];
+ set(ax, 'Position', position)
+
+ if (conf.show_labels)
+ set(t, 'Units', 'centimeters')
+ position = [1, 0.25, img_size(1), 0.75];
+ set(t, 'Position', position)
+ end
+ end
+end
diff --git a/zUtil_Deformation/plotting/gt6DMakeClusterODFFigureForPaper.m b/zUtil_Deformation/plotting/gt6DMakeClusterODFFigureForPaper.m
new file mode 100644
index 00000000..c5962d3e
--- /dev/null
+++ b/zUtil_Deformation/plotting/gt6DMakeClusterODFFigureForPaper.m
@@ -0,0 +1,143 @@
+function gt6DMakeClusterODFFigureForPaper(cluster, cluster_rec, grs, varargin)
+% function gt6DMakeClusterODFFigureForPaper(cluster, cluster_rec, grs, varargin)
+
+ conf = struct( ...
+ 'percent', 0.0025, ...
+ 'filename', '', ...
+ 'clims', [], ...
+ 'pixel_to_cm', 0.5, ...
+ 'colorbar', 'no' );
+ conf = parse_pv_pairs(conf, varargin);
+
+ if (~exist('cluster_rec', 'var') || isempty(cluster_rec))
+ cluster_rec = gtLoadClusterRec(cluster.phaseid, cluster.gids);
+ end
+ if (~exist('grs', 'var') || isempty(grs))
+ grs = gtLoadGrain(cluster.phaseid, cluster.gids);
+ end
+
+ internal_shift = cluster_rec.SEG.segbb(1:3) - cluster_rec.ODF6D.shift + 1;
+ seg_vol_bb = [internal_shift, cluster_rec.SEG.segbb(4:6)];
+
+ dm_vol(:, :, :, 3) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 3), seg_vol_bb);
+ dm_vol(:, :, :, 2) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 2), seg_vol_bb);
+ dm_vol(:, :, :, 1) = gtCrop(cluster_rec.ODF6D.voxels_avg_R_vectors(:, :, :, 1), seg_vol_bb);
+
+ int_vol = gtCrop(cluster_rec.ODF6D.intensity, seg_vol_bb);
+
+ gv_dm = gtDefDmvol2Gvdm(dm_vol);
+ gv_mask = logical(cluster_rec.SEG.seg(:));
+ gv_int = int_vol(:);
+
+ p = gtLoadParameters();
+ resolution = tand(p.labgeo.omstep/2);
+ grid_points = [ ...
+ min(cluster_rec.ODF6D.R_vectors{1}, [], 1), ...
+ max(cluster_rec.ODF6D.R_vectors{1}, [], 1), ...
+ resolution([1 1 1])];
+ grid_points(1:3) = grid_points(1:3) - mod(grid_points(1:3), resolution);
+ grid_points(4:6) = grid_points(4:6) + mod(resolution - mod(grid_points(4:6), resolution), resolution);
+ odf = gtGetODFFromGvdm(gv_dm(:, gv_mask), grid_points, gv_int(gv_mask));
+
+% x_pos = 2 * atand(linspace(grid_points(1), grid_points(4), size(odf, 1)) - grs(1).R_vector(1));
+% y_pos = 2 * atand(linspace(grid_points(2), grid_points(5), size(odf, 2)) - grs(1).R_vector(2));
+% z_pos = 2 * atand(linspace(grid_points(3), grid_points(6), size(odf, 3)) - grs(1).R_vector(3));
+
+ x_pos = linspace(grid_points(1), grid_points(4), size(odf, 1));
+ y_pos = linspace(grid_points(2), grid_points(5), size(odf, 2));
+ z_pos = linspace(grid_points(3), grid_points(6), size(odf, 3));
+
+ f = figure();
+ ax = axes('parent', f);
+ thr_value = (max(odf(:)) - min(odf(:))) * conf.percent + min(odf(:));
+ p = patch( ...
+ isosurface(x_pos, y_pos, z_pos, permute(odf, [2 1 3]), thr_value), ...
+ 'FaceVertexAlphaData', 0.2, 'FaceAlpha', 'flat', 'parent', ax);
+ set(p, 'FaceColor', 'cyan', 'EdgeColor', 'none')
+ camlight('right')
+ camlight('left')
+ lighting('gouraud')
+ grid(ax, 'on')
+ view(ax, 3);
+
+ r_vecs = cat(1, grs(:).R_vector);
+ hold(ax, 'on')
+ scatter3(ax, r_vecs(:, 1), r_vecs(:, 2), r_vecs(:, 3), 60, 'red', 'filled')
+ hold(ax, 'off')
+
+ xlabel(ax, 'X');
+ ylabel(ax, 'Y');
+ zlabel(ax, 'Z');
+
+ for ii = 1:numel(grs)
+ text(r_vecs(ii, 1), r_vecs(ii, 2), r_vecs(ii, 3), ...
+ sprintf(' \\leftarrow %d', grs(ii).id), 'parent', ax)
+ end
+
+% for ii = 1:numel(grs)
+% if (grs(ii).id == 171)
+% text(r_vecs(ii, 1), r_vecs(ii, 2), r_vecs(ii, 3), ...
+% sprintf('%d \\rightarrow ', grs(ii).id), 'parent', ax, ...
+% 'HorizontalAlignment', 'right')
+% elseif (grs(ii).id == 3)
+% text(r_vecs(ii, 1), r_vecs(ii, 2), r_vecs(ii, 3), ...
+% sprintf('%d \\rightarrow ', grs(ii).id), 'parent', ax, ...
+% 'HorizontalAlignment', 'right')
+% elseif (grs(ii).id == 67)
+% text(r_vecs(ii, 1), r_vecs(ii, 2), r_vecs(ii, 3), ...
+% sprintf(' \\leftarrow %d', grs(ii).id), 'parent', ax)
+% elseif (grs(ii).id == 200)
+% text(r_vecs(ii, 1), r_vecs(ii, 2), r_vecs(ii, 3), ...
+% sprintf(' \\leftarrow %d', grs(ii).id), 'parent', ax)
+% else
+% text(r_vecs(ii, 1), r_vecs(ii, 2), r_vecs(ii, 3), ...
+% sprintf(' \\leftarrow %d', grs(ii).id), 'parent', ax)
+% end
+% end
+
+ set_size(f, ax, conf, odf);
+
+ drawnow();
+
+ if (~isempty(conf.filename) && strcmpi(conf.filename, 'preview'))
+ [filename, filedir] = uigetfile({'*.png'; '*.eps'});
+ if (filename)
+ conf.filename = fullfile(filedir, filename);
+ else
+ conf.filename = [];
+ end
+ end
+
+ if (~isempty(conf.filename))
+ [~, ~, ext] = fileparts(conf.filename);
+ if (isempty(ext))
+ saveas(f, [conf.filename '.eps']);
+ saveas(f, [conf.filename '.png']);
+ else
+ saveas(f, conf.filename);
+ end
+ end
+end
+
+function set_size(f, ax, conf, odf)
+ set(f, 'Units', 'centimeters')
+ img_size = mean(size(odf)) * conf.pixel_to_cm;
+ img_size = img_size([1 1]);
+ set(ax, 'Units', 'centimeters')
+ if (strcmpi(conf.colorbar, 'no'))
+ position = [0, 0, img_size] + [0, 0, 4, 1.5];
+ set(f, 'Position', position)
+ set(f, 'Paperposition', position)
+ else
+ position = [0, 0, img_size] + [0, 0, 5, 2];
+ set(f, 'Position', position)
+ set(f, 'Paperposition', position)
+
+ cb = colorbar('peer', ax, 'location', 'EastOutside');
+ set(cb, 'Units', 'centimeters')
+ position = [img_size(1)+2.35, 1, 0.65, img_size(2)];
+ set(cb, 'Position', position)
+ end
+ position = [2, 1, img_size];
+ set(ax, 'Position', position)
+end
--
GitLab