From fbc296e1a093b3d2550b35e6b10dd49d185b772c Mon Sep 17 00:00:00 2001
From: Nicola Vigano <nicola.vigano@esrf.fr>
Date: Wed, 4 Feb 2015 18:04:54 +0100
Subject: [PATCH] Figures: added function for generating figures for papers
Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>
---
.../plotting/gt6DMakePhaseFigureForPaper.m | 178 ++++++++++++++++++
1 file changed, 178 insertions(+)
create mode 100644 zUtil_Deformation/plotting/gt6DMakePhaseFigureForPaper.m
diff --git a/zUtil_Deformation/plotting/gt6DMakePhaseFigureForPaper.m b/zUtil_Deformation/plotting/gt6DMakePhaseFigureForPaper.m
new file mode 100644
index 00000000..4265f208
--- /dev/null
+++ b/zUtil_Deformation/plotting/gt6DMakePhaseFigureForPaper.m
@@ -0,0 +1,178 @@
+function gt6DMakePhaseFigureForPaper( phase_mat, phase_id, varargin )
+% gtCSMakeFigureForPaper( phase_mat, phase_id, varargin )
+% conf = struct( ...
+% 'use_dmvol', true, ...
+% 'abs_vol', [], ...
+% 'abs_mask', [], ...
+% 'filename', '', ...
+% 'plane', 'xy', ...
+% 'flip_ud', false, ...
+% 'flip_lr', false, ...
+% 'slice', 1, ...
+% 'clims', [], ...
+% 'pixel_to_cm', 0.05, ...
+% 'borders', 'no', ...
+% 'colorbar', 'no');
+%
+
+ conf = struct( ...
+ 'use_dmvol', true, ...
+ 'abs_vol', [], ...
+ 'abs_mask', [], ...
+ 'filename', '', ...
+ 'plane', 'xy', ...
+ 'flip_ud', false, ...
+ 'flip_lr', false, ...
+ 'slice', 1, ...
+ 'clims', [], ...
+ 'pixel_to_cm', 0.05, ...
+ 'borders', 'no', ...
+ 'colorbar', 'no' );
+ conf = parse_pv_pairs(conf, varargin);
+
+ slice_ids = get_slice(phase_mat.vol, conf.plane, conf.slice);
+ if (conf.use_dmvol && isfield(phase_mat, 'dmvol'))
+ slice_rod = get_slice(phase_mat.dmvol, conf.plane, conf.slice);
+ indx = find(slice_ids > 0);
+ r_vecs = reshape(slice_rod, [], 3);
+ r_vecs = r_vecs(indx, :);
+
+ cmap = get_cmap(r_vecs, phase_id);
+
+ slice_R = zeros(size(slice_ids));
+ slice_G = zeros(size(slice_ids));
+ slice_B = zeros(size(slice_ids));
+
+ slice_R(indx) = cmap(:, 1);
+ slice_G(indx) = cmap(:, 2);
+ slice_B(indx) = cmap(:, 3);
+ else
+ sample = GtSample.loadFromFile();
+
+ gids = sort(unique(slice_ids));
+ gids(gids < 1) = [];
+ r_vecs = sample.phases{phase_id}.R_vector(gids, :);
+
+ cmap = get_cmap(r_vecs, phase_id);
+
+ slice_R = zeros(size(slice_ids));
+ slice_G = zeros(size(slice_ids));
+ slice_B = zeros(size(slice_ids));
+ for ii = 1:numel(gids)
+ indx = find(slice_ids == gids(ii));
+ slice_R(indx) = cmap(ii, 1);
+ slice_G(indx) = cmap(ii, 2);
+ slice_B(indx) = cmap(ii, 3);
+ end
+ end
+
+ slice_abs = get_slice(conf.abs_vol, conf.plane, conf.slice);
+ slice_abs = (slice_abs - min(slice_abs(:))) ./ (max(slice_abs(:)) - min(slice_abs(:)));
+
+ slice_mask = get_slice(conf.abs_mask, conf.plane, conf.slice);
+ slice_R(~slice_mask) = slice_abs(~slice_mask);
+ slice_G(~slice_mask) = slice_abs(~slice_mask);
+ slice_B(~slice_mask) = slice_abs(~slice_mask);
+
+ % 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);
+ end
+ if (conf.flip_lr)
+ slice_R = flipud(slice_R);
+ slice_G = flipud(slice_G);
+ slice_B = flipud(slice_B);
+ end
+
+ f = figure();
+ ax = axes('Parent', f);
+ im = imagesc(cat(3, slice_R', slice_G', slice_B'), '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;
+ 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, 2];
+ 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
+
+ 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 cmap = get_cmap(r_vecs, phase_id)
+ p = gtLoadParameters();
+ cryst_system = p.cryst(phase_id).crystal_system;
+ cryst_spacegroup = p.cryst(phase_id).spacegroup;
+ symm = gtCrystGetSymmetryOperators(cryst_system, cryst_spacegroup);
+
+ [cmap, ~, ~] = gtIPFCmap(phase_id, [], ...
+ 'r_vectors', r_vecs, ...
+ 'crystal_system', cryst_system, ...
+ 'background', false, ...
+ 'symm', symm);
+end
+
+
--
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