Gui: added new tool for visualizing orientations in reconstructions

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

zUtil_TomoUtils/GtRodriguesVolView.m

+classdef GtRodriguesVolView < GtVolView
+    properties
+        r_vecs = [];
+
+        mask = [];
+        threshold = 0;
+
+        p = gtLoadParameters();
+        phase_id = 1;
+        symm;
+    end
+
+    methods (Access = public)
+        function self = GtRodriguesVolView(r_vecs_in, intensities, varargin)
+            self = self@GtVolView(intensities, varargin{:});
+            [self, ~] = parse_pv_pairs(self, varargin);
+
+            % Should be in initGui, bu some parameters will not be ready by
+            % then
+            self.conf.h_overlay = [];
+
+            cryst_system = self.p.cryst(self.phase_id).crystal_system;
+            cryst_spacegroup = self.p.cryst(self.phase_id).spacegroup;
+            self.symm = gtCrystGetSymmetryOperators(cryst_system, cryst_spacegroup);
+
+            if (isempty(self.mask))
+                self.mask = intensities > self.threshold;
+            end
+            self.r_vecs = r_vecs_in;
+        end
+    end
+
+    methods (Access = protected)
+        function initGui(self)
+            self.initGui@GtVolView();
+
+            self.conf.h_overlay = [];
+        end
+
+        function slice = loadSlice(self, vol)
+        % GTVOLVIEW/LOADSLICE Loads a slice from the volume (given the plane and
+        % slice index in obj.conf.*) and permutes it to be visualised correctly
+        % by matlab, which always flips X and Y dimensions in visualisation.
+
+            if (isempty(self.mask))
+                slice(:, :, 4) = self.loadSlice@GtVolView(zeros(size(vol)));
+            else
+                slice(:, :, 4) = double(self.loadSlice@GtVolView(self.mask));
+            end
+
+            if (~isempty(self.r_vecs))
+                slice(:, :, 1) = self.loadSlice@GtVolView(self.r_vecs(:, :, :, 1));
+                slice(:, :, 2) = self.loadSlice@GtVolView(self.r_vecs(:, :, :, 2));
+                slice(:, :, 3) = self.loadSlice@GtVolView(self.r_vecs(:, :, :, 3));
+            end
+        end
+
+        function setVisualisedData(self, image, vol, is_overlay)
+        % GTVOLVIEW/SETVISUALISEDDATA Loads a slice and then operates
+        % transformations on them, to adapt to the requested visualization needs
+
+            slice = self.loadSlice(vol);
+
+            if (~is_overlay)
+                avg_R_vecs = slice(:, :, 1:3);
+                mask_slice =  slice(:, :, 4);
+                indx = find(mask_slice(:));
+                avg_R_vecs = permute(avg_R_vecs, [3 1 2]);
+                avg_R_vecs = reshape(avg_R_vecs, 3, [])';
+                avg_R_vecs = avg_R_vecs(indx, :);
+
+                if (~isempty(avg_R_vecs))
+                    [cmap, ~, ~] = gtIPFCmap(self.phase_id, [], ...
+                        'r_vectors', avg_R_vecs, ...
+                        'crystal_system', self.p.cryst(self.phase_id).crystal_system, ...
+                        'symm', self.symm);
+                    cmap = cmap(2:end, :);
+
+                    img_slice_R = zeros(size(mask_slice));
+                    img_slice_G = zeros(size(mask_slice));
+                    img_slice_B = zeros(size(mask_slice));
+
+                    img_slice_R(indx) = cmap(:, 1);
+                    img_slice_G(indx) = cmap(:, 2);
+                    img_slice_B(indx) = cmap(:, 3);
+
+                    set(image, 'CData', cat(3, img_slice_R, img_slice_G, img_slice_B));
+                end
+            end
+        end
+    end
+end
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