Fix plots found while reviewing the generated docs images

CHANGELOG.md

@@ -21,6 +21,12 @@ Notable changes to ORTools are listed here. The format follows
 - Documentation dependencies are pinned in `docs/requirements.txt`.
 
 ### Fixed
+- `plotMap_KSvariantPairs` with `parentGrainId` shows only the chosen parent grain instead of the
+  whole map in grey.
+- `plotMap_blockWidths` draws the mean of the projected points as lines again and no longer marks
+  every grain centre (MTEX 7 defaults).
+- `plotPDF_variants`, `plotPDF_packets` and `plotPDF_bain` use one colour per Id in the colorbar,
+  as the corresponding maps do.
 - Broken links to examples 1 and 2 in the documentation.
 - `plotCrystal_OR` help text named the wrong function and input.
 

docs/function_index.md

@@ -231,6 +231,20 @@ This function is a GUI to to define an orientation relationship (OR) with parall
   <img src="../images/guiOR.png" alt="UI of guiOR" width="600"/>
 </p>
 
+## L
+
+### <a id="liftAboveMap"></a>liftAboveMap
+
+This auxiliary function lifts arrows drawn with *quiver(grains,...)* slightly towards the viewer. MTEX 7 draws these arrows in 3D, so arrows lying in the plane of the map would otherwise be hidden by the map itself.
+
+- Syntax
+  - h = liftAboveMap(h,grains)
+- Input
+  - h       - handle(s) returned by quiver(grains,...)
+  - grains  - @grain2d passed to quiver
+- Output
+  - h       - the same handle(s)
+
 ## O
 
 ### <a id="orientationMaker"></a>orientationMaker

src/microstructureHierarchy/computeHabitPlane.m

@@ -125,7 +125,8 @@
                     pIds = pGrainId(isTrace);
                     cIds = cGrains(ismember(idx(:, 1), pIds) & cGrains.variantId == ii).id;
                     [~, idxTraces] = ismember(job.mergeId(cIds), pGrainId);
-                    q = quiver(cGrains(ismember(cGrains.id, cIds)), traces.child(idxTraces, ii), 'color', linecolor);
+                    q = quiver(cGrains(ismember(cGrains.id, cIds)), traces.child(idxTraces, ii), 'color', linecolor, 'noMarker');
+                    liftAboveMap(q, cGrains(ismember(cGrains.id, cIds)));
                     q.ShowArrowHead = 'off'; q.Marker = 'none';
                 end
                 colorbar;
@@ -162,7 +163,8 @@
                     plot(cEBSD(ismember(cEBSD.id, cIds)), repmat(cmap(ii, :), [length(cIds) 1]));
                     hold all
                     [~, mP] = plot(pGrains.boundary);
-                    q = quiver(pGrains(ismember(pGrains.id, unique(pIds))), traces.child(unique(idxTraces), ii), 'color', linecolor);
+                    q = quiver(pGrains(ismember(pGrains.id, unique(pIds))), traces.child(unique(idxTraces), ii), 'color', linecolor, 'noMarker');
+                    liftAboveMap(q, pGrains(ismember(pGrains.id, unique(pIds))));
                     q.ShowArrowHead = 'off'; q.Marker = 'none';
                     hold off
                     set(figH, 'Name', strcat(['Variant ', num2str(ii)]), 'NumberTitle', 'on');
@@ -274,7 +276,8 @@
                     pIds = pGrainId(isTrace);
                     cIds = cGrains(ismember(idx(:, 1), pIds) & cGrains.variantId == ii).id;
                     [~, idxTraces] = ismember(job.mergeId(cIds), pGrainId);
-                    q = quiver(cGrains(ismember(cGrains.id, cIds)), traces.imagePlane(idxTraces, ii), 'color', linecolor);
+                    q = quiver(cGrains(ismember(cGrains.id, cIds)), traces.imagePlane(idxTraces, ii), 'color', linecolor, 'noMarker');
+                    liftAboveMap(q, cGrains(ismember(cGrains.id, cIds)));
                     q.ShowArrowHead = 'off'; q.Marker = 'none';
                 end
                 hold off
@@ -336,7 +339,8 @@
                     isTrace = ~isnan(traces.imagePlane(:, ii));
                     pIds = pGrainId(isTrace);
                     [~, idxTraces] = ismember(pIds, pGrainId);
-                    q = quiver(pGrains(ismember(pGrains.id, unique(pIds))), traces.imagePlane(unique(idxTraces), ii), 'color', linecolor);
+                    q = quiver(pGrains(ismember(pGrains.id, unique(pIds))), traces.imagePlane(unique(idxTraces), ii), 'color', linecolor, 'noMarker');
+                    liftAboveMap(q, pGrains(ismember(pGrains.id, unique(pIds))));
                     q.ShowArrowHead = 'off'; q.Marker = 'none';
                     hold off
                     set(figH, 'Name', strcat(['Variant ', num2str(ii)]), 'NumberTitle', 'on');

src/microstructureHierarchy/plotMap_KSvariantPairs.m

@@ -41,6 +41,8 @@
     if pGrainId
         [grainsTemp, ebsdTemp] = computeVariantGrains(job, 'parentGrainId', pGrainId);
         pGrain = job.parentGrains(job.parentGrains.id == pGrainId);
+        % Only show the map data of the chosen parent grain
+        ebsdTemp = ebsdTemp(ismember(ebsdTemp.id, job.ebsd(pGrain).id));
     else
         warning('Argument ''parentGrainId'' not specified. Equivalent variant pairs will be calculated for the EBSD map.');
         [grainsTemp, ebsdTemp] = computeVariantGrains(job);
@@ -127,8 +129,11 @@
     if ~isempty(varargin) && any(strcmpi(varargin, 'parentGrainId'))
         plot(pGrain.boundary, varargin{:}, 'linecolor', [0.45 0.45 0.45], varargin{:});
     end
-    [hL(end + 1), mP] = plot(job.grains.boundary, varargin{:});
-    hL(end).FaceColor = 'k';
+    % With a parent grain, only its own outline (above) is drawn
+    if isempty(pGrainId)
+        [hL(end + 1), mP] = plot(job.grains.boundary, varargin{:});
+        hL(end).FaceColor = 'k';
+    end
     hold off
     legend
     set(figH, 'Name', 'Map: Equivalent variant pair Boundaries', 'NumberTitle', 'on');

src/microstructureHierarchy/plotMap_blockWidths.m

@@ -90,9 +90,13 @@
     if length(pGrainId) == 1
         [~, mP] = plot(cGrains, dBlock, varargin{:});
         hold all
-        ha(1) = quiver(squeeze(cGrains), squeeze(cross(zz, zvector)), 'color', [1 0 0]);
-        ha(2) = quiver(squeeze(cGrains), squeeze(zz), 'color', [0 1 0]);
-        ha(3) = quiver(squeeze(cGrains), squeeze(new_A_vec), 'color', [0 0 1]);
+        % MTEX 7 marks the grain centres by default ('noMarker' switches that
+        % off) and hides arrows lying in the map plane (liftAboveMap); the
+        % mean of the projected points is an axis, drawn as a line
+        ha(1) = quiver(squeeze(cGrains), squeeze(cross(zz, zvector)), 'color', [1 0 0], 'noMarker');
+        ha(2) = quiver(squeeze(cGrains), squeeze(zz), 'color', [0 1 0], 'noMarker');
+        ha(3) = quiver(squeeze(cGrains), squeeze(new_A_vec), 'color', [0 0 1], 'noMarker', 'antipodal');
+        liftAboveMap(ha, squeeze(cGrains));
         legend(ha, '$111_a {\parallel} 011_m$ trace', '$111_a {\parallel} 011_m$ normal', 'Mean of projected points')
     else
         for ii = 1:length(cGrains)

src/microstructureHierarchy/plotPDF_bain.m

@@ -43,11 +43,13 @@ function plotPDF_bain(job, varargin)
 
     % Define the maximum number of color levels and plot the colorbar
     maxColors = max(bainIds);
+    % One colour per Id, as in the maps
+    cmap = cmap(round(linspace(1, size(cmap, 1), maxColors)), :);
     colormap(cmap);
-    caxis([1 maxColors]);
+    caxis([0.5 maxColors + 0.5]);
     colorbar('location', 'eastOutSide', 'LineWidth', 1.25, 'TickLength', 0.01, ...
              'YTick', [1:1:maxColors], ...
-             'YTickLabel', num2str([1:1:maxColors]'), 'YLim', [1 maxColors], ...
+             'YTickLabel', num2str([1:1:maxColors]'), 'YLim', [0.5 maxColors + 0.5], ...
              'TickLabelInterpreter', 'latex', 'FontName', 'Helvetica', 'FontSize', 14, 'FontWeight', 'bold');
     hold on
 

src/microstructureHierarchy/plotPDF_packets.m

@@ -43,11 +43,13 @@ function plotPDF_packets(job, varargin)
 
     % Define the maximum number of color levels and plot the colorbar
     maxColors = max(packIds);
+    % One colour per Id, as in the maps
+    cmap = cmap(round(linspace(1, size(cmap, 1), maxColors)), :);
     colormap(cmap);
-    caxis([1 maxColors]);
+    caxis([0.5 maxColors + 0.5]);
     colorbar('location', 'eastOutSide', 'LineWidth', 1.25, 'TickLength', 0.01, ...
              'YTick', [1:1:maxColors], ...
-             'YTickLabel', num2str([1:1:maxColors]'), 'YLim', [1 maxColors], ...
+             'YTickLabel', num2str([1:1:maxColors]'), 'YLim', [0.5 maxColors + 0.5], ...
              'TickLabelInterpreter', 'latex', 'FontName', 'Helvetica', 'FontSize', 14, 'FontWeight', 'bold');
     hold on
 

src/microstructureHierarchy/plotPDF_variants.m

@@ -44,11 +44,13 @@ function plotPDF_variants(job, varargin)
 
     % Define the maximum number of color levels and plot the colorbar
     maxColors = length(oriVariants);
+    % One colour per Id, as in the maps
+    cmap = cmap(round(linspace(1, size(cmap, 1), maxColors)), :);
     colormap(cmap);
-    caxis([1 maxColors]);
+    caxis([0.5 maxColors + 0.5]);
     colorbar('location', 'eastOutSide', 'LineWidth', 1.25, 'TickLength', 0.01, ...
              'YTick', [1:1:maxColors], ...
-             'YTickLabel', num2str([1:1:maxColors]'), 'YLim', [1 maxColors], ...
+             'YTickLabel', num2str([1:1:maxColors]'), 'YLim', [0.5 maxColors + 0.5], ...
              'TickLabelInterpreter', 'latex', 'FontName', 'Helvetica', 'FontSize', 14, 'FontWeight', 'bold');
     hold on
 

src/util/liftAboveMap.m

@@ -0,0 +1,31 @@
+function h = liftAboveMap(h, grains)
+    %% Function description:
+    % This function lifts arrows drawn with "quiver(grains,...)" slightly
+    % towards the viewer. MTEX 7 draws these arrows in 3D, so arrows lying
+    % in the plane of the map are hidden by the map itself and only their
+    % heads remain visible.
+    %
+    %% Syntax:
+    %  h = liftAboveMap(h,grains)
+    %
+    %% Input:
+    %  h      - handle(s) returned by quiver(grains,...)
+    %  grains - @grain2d passed to quiver
+    %
+    %% Output:
+    %  h      - the same handle(s)
+
+    if isempty(h), return; end
+
+    outOfScreen = grains.how2plot.outOfScreen;
+    ax = ancestor(h(1), 'axes');
+    dz = 0.01 * max(diff(ax.XLim), diff(ax.YLim)) * outOfScreen.z;
+    for ii = 1:numel(h)
+        if isprop(h(ii), 'ZData')
+            if isempty(h(ii).ZData)
+                h(ii).ZData = zeros(size(h(ii).XData));
+            end
+            h(ii).ZData = h(ii).ZData + dz;
+        end
+    end
+end