Fixed some figure creation functions

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

zUtil_Drawing/gtFigureCreateClusterIPF.m

@@ -35,6 +35,8 @@ function gtFigureCreateClusterIPF(cluster, cluster_rec, varargin)
         'rotation_angle', zeros(0, 1), ...
         'borders', false, ...
         'colorbar', false, ...
+        'pixel_size', [], ...
+        'tight', [], ...
         'extras', [] );
     conf = parse_pv_pairs(conf, varargin);
 
@@ -91,8 +93,8 @@ function gtFigureCreateClusterIPF(cluster, cluster_rec, varargin)
     slice_B(slice_seg(:)) = cmap(:, 3);
 
     int_vol = gtCrop(cluster_rec.ODF6D.intensity, seg_vol_bb) .* seg_vol;
-    slice_int_vol = gtVolumeGetSlice(int_vol, conf.plane, conf.slice, true);
-    slice_dm_vol = gtVolumeGetSlice(dm_vol, conf.plane, conf.slice, true);
+    slice_int_vol = gtVolumeGetSlice(int_vol, conf.plane, conf.slice, false);
+    slice_dm_vol = gtVolumeGetSlice(dm_vol, conf.plane, conf.slice, false);
 
     % needed for the high anglular boundaries
     [slice_kam, slice_gam] = gtDefComputeKernelAverageMisorientation(slice_dm_vol, slice_int_vol);
@@ -101,8 +103,7 @@ function gtFigureCreateClusterIPF(cluster, cluster_rec, varargin)
 
     %
 
-    % Note the inversion between lr/up because of matlab's transpose problem
-    if (conf.flip_ud)
+    if (conf.flip_lr)
         slice_R = fliplr(slice_R);
         slice_G = fliplr(slice_G);
         slice_B = fliplr(slice_B);
@@ -110,7 +111,7 @@ function gtFigureCreateClusterIPF(cluster, cluster_rec, varargin)
         slice_seg = fliplr(slice_seg);
         slice_kam = fliplr(slice_kam);
     end
-    if (conf.flip_lr)
+    if (conf.flip_ud)
         slice_R = flipud(slice_R);
         slice_G = flipud(slice_G);
         slice_B = flipud(slice_B);
@@ -136,6 +137,33 @@ function gtFigureCreateClusterIPF(cluster, cluster_rec, varargin)
     slice_skel(slice_kam_skel) = 0.5;
     slice_skel(slice_kam_skel_high) = 0;
 
+    if (~isempty(conf.tight))
+        first_ind_1 = find(sum(slice_seg, 2), 1, 'first');
+        last_ind_1 = find(sum(slice_seg, 2), 1, 'last');
+
+        first_ind_2 = find(sum(slice_seg, 1), 1, 'first');
+        last_ind_2 = find(sum(slice_seg, 1), 1, 'last');
+
+        slice_img = slice_img(first_ind_1:last_ind_1, first_ind_2:last_ind_2, :);
+        slice_skel = slice_skel(first_ind_1:last_ind_1, first_ind_2:last_ind_2);
+        slice_seg = slice_seg(first_ind_1:last_ind_1, first_ind_2:last_ind_2);
+
+        if (numel(conf.tight) == 1)
+            conf.tight = conf.tight([1 1; 1 1]);
+        elseif (size(conf.tight, 1) == 1)
+            conf.tight = conf.tight([1 1], :);
+        elseif (size(conf.tight, 2) == 1)
+            conf.tight = conf.tight(:, [1 1]);
+        end
+
+        slice_img = padarray(slice_img, conf.tight(:, 1), 0, 'pre');
+        slice_skel = padarray(slice_skel, conf.tight(:, 1), 1, 'pre');
+        slice_seg = padarray(slice_seg, conf.tight(:, 1), false, 'pre');
+        slice_img = padarray(slice_img, conf.tight(:, 2), 0, 'post');
+        slice_skel = padarray(slice_skel, conf.tight(:, 2), 1, 'post');
+        slice_seg = padarray(slice_seg, conf.tight(:, 2), false, 'post');
+    end
+
     f = figure();
     ax = axes('parent', f);
     imagesc(slice_img, 'parent', ax, ...

zUtil_Drawing/gtFigureCreateClusterKAM.m

@@ -29,12 +29,14 @@ function gtFigureCreateClusterKAM(cl, cl_rec, grs, varargin)
         'slice', 1, ...
         'clims', [0 1], ...
         'show_labels', false, ...
+        'label', [], ...
         'pixel_to_cm', 0.1, ...
         'rotation_axes', [0 0 1], ...
         'rotation_angles', zeros(0, 1), ...
         'use_slice_R_vector', false, ...
         'borders', true, ...
         'colorbar', true, ...
+        'tight', [], ...
         'extras', [] );
     conf = parse_pv_pairs(conf, varargin);
 
@@ -113,13 +115,12 @@ function gtFigureCreateClusterKAM(cl, cl_rec, grs, varargin)
     slice_igm = slice_igm(vert_lims(1):vert_lims(2), horz_lims(1):horz_lims(2));
     slice_seg = slice_seg(vert_lims(1):vert_lims(2), horz_lims(1):horz_lims(2));
 
-    % Note the inversion between lr/up because of matlab's transpose problem
-    if (conf.flip_ud)
+    if (conf.flip_lr)
         slice_kam = fliplr(slice_kam);
         slice_igm = fliplr(slice_igm);
         slice_seg = fliplr(slice_seg);
     end
-    if (conf.flip_lr)
+    if (conf.flip_ud)
         slice_kam = flipud(slice_kam);
         slice_igm = flipud(slice_igm);
         slice_seg = flipud(slice_seg);
@@ -132,14 +133,30 @@ function gtFigureCreateClusterKAM(cl, cl_rec, grs, varargin)
 
     %
 
+    if (~isempty(conf.tight))
+        if (numel(conf.tight) == 1)
+            conf.tight = conf.tight([1 1; 1 1]);
+        elseif (size(conf.tight, 1) == 1)
+            conf.tight = conf.tight([1 1], :);
+        elseif (size(conf.tight, 2) == 1)
+            conf.tight = conf.tight(:, [1 1]);
+        end
+        slice_kam = padarray(slice_kam, conf.tight(:, 1), 0, 'pre');
+        slice_igm = padarray(slice_igm, conf.tight(:, 1), 0, 'pre');
+        slice_seg = padarray(slice_seg, conf.tight(:, 1), false, 'pre');
+        slice_kam = padarray(slice_kam, conf.tight(:, 2), 0, 'post');
+        slice_igm = padarray(slice_igm, conf.tight(:, 2), 0, 'post');
+        slice_seg = padarray(slice_seg, conf.tight(:, 2), false, 'post');
+    end
+
     img_size = [size(slice_seg, 2), size(slice_seg, 1)];
 
     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', ...
+    imagesc(slice_kam, 'parent', ax, ...
+        'AlphaDataMapping', 'scaled', 'AlphaData', slice_seg, ...
         clims_kam );
     colormap(ax, jet)
 
@@ -167,8 +184,8 @@ function gtFigureCreateClusterKAM(cl, cl_rec, grs, varargin)
 
     f = figure();
     ax = axes('parent', f);
-    imagesc(slice_igm', 'parent', ax, ...
-        'AlphaDataMapping', 'scaled', 'AlphaData', slice_seg', ...
+    imagesc(slice_igm, 'parent', ax, ...
+        'AlphaDataMapping', 'scaled', 'AlphaData', slice_seg, ...
         clims_igm );
     colormap(ax, jet);
 

zUtil_Imaging/gtVolumeGetSlice.m

-function slice = gtVolumeGetSlice(vol, plane, slice_idx)
+function slice = gtVolumeGetSlice(vol, plane, slice_idx, do_squeeze)
     switch (lower(plane))
         case 'xy'
             slice = vol(:, :, slice_idx, :);
         case 'yx'
             slice = permute(vol(:, :, slice_idx, :), [2 1 3 4]);
         case 'yz'
-            slice = squeeze(vol(slice_idx, :, :, :));
+            slice = vol(slice_idx, :, :, :);
         case 'zy'
-            slice = permute(squeeze(vol(slice_idx, :, :, :)), [2 1 3 4]);
+            slice = permute(vol(slice_idx, :, :, :), [2 1 3 4]);
         case 'xz'
-            slice = squeeze(vol(:, slice_idx, :, :));
+            slice = vol(:, slice_idx, :, :);
         case 'zx'
-            slice = permute(squeeze(vol(:, slice_idx, :, :)), [2 1 3 4]);
+            slice = permute(vol(:, slice_idx, :, :), [2 1 3 4]);
+    end
+    if (~exist('do_squeeze', 'var') || isempty(do_squeeze) || do_squeeze)
+        slice = squeeze(slice);
     end
 end
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