some pollishing

examples/GrainReconstructionDemo.m

@@ -0,0 +1,93 @@
+%% 
+
+
+%% Import some EBSD data
+
+mtexdata forsterite
+plotx2east
+
+plot(ebsd)
+
+%% First attempt on grain reconstruction
+
+[grains,ebsd.grainId] = calcGrains(ebsd,'angle',5*degree);
+
+plot(grains)
+
+
+%%
+% The resulting grains contain a lot of holes and one pixel grains due to
+% misindexing. A good measure for regions where indexing went wrong is the
+% band contrast
+
+plot(ebsd,ebsd.bc)
+
+%%
+% We see its quite low at the grain boundaries and, e.g., in the top left
+% rectangle. Lets set the phase of measurements with bandcontrast
+% smaller then a certain threshold to notIndexed
+
+condition = ebsd.bc < 80;
+
+% setting the phase to zero means notIndexed
+ebsd(condition).phase = 0
+plot(ebsd)
+
+
+%%
+
+[grains,ebsd.grainId] = calcGrains(ebsd,'angle',5*degree);
+
+plot(grains)
+
+
+%%
+
+plot(grains,log(grains.grainSize ./ grains.boundarySize))
+colorbar
+
+%%
+% remove 
+
+ind = ~grains.isIndexed & log(grains.grainSize ./ grains.boundarySize) < -0.4;
+
+plot(ebsd)
+hold on
+plot(grains(ind),'faceColor',[0 0 0],'DisplayName','fill this')
+hold off
+
+% remove marked measurements
+ebsd(grains(ind)) = []
+
+%%
+
+[grains,ebsd.grainId] = calcGrains(ebsd,'angle',5*degree);
+
+plot(grains)
+
+%%
+% fill grains that are to small
+
+ind = grains.grainSize < 5;
+
+hold on
+plot(grains(ind),'faceColor',[0 0 0],'DisplayName','fill this')
+hold off
+
+% remove marked measurements
+ebsd(grains(ind)) = []
+
+%%
+% 
+
+[grains,ebsd.grainId] = calcGrains(ebsd,'angle',5*degree);
+
+plot(grains)
+
+
+
+%% Smooth grains
+
+grains = smooth(grains,2);
+
+plot(grains)

geometry/@DelaunaySO3/display.m

@@ -8,8 +8,8 @@ function display(DSO3)
 
 disp(['  size: ' size2str(DSO3)]);
 disp(['  tetrahegons: ',int2str(size(DSO3.tetra,1))]);
-disp(['  ' char(DSO3.CS,'verbose'));
-disp(['  ' char(DSO3.SS,'verbose'));
+disp(['  ' char(DSO3.CS,'verbose')]);
+disp(['  ' char(DSO3.SS,'verbose')]);
 
 if length(DSO3) < 30 && ~isempty(o), Euler(DSO3);end
 

help/doc/UsersGuide/EBSDAnalysis/EBSDSpatialPlots.m

@@ -198,7 +198,7 @@
 % Suppose the mode of the ODF somewhere in our spatial distribution of
 % grains (the orientation map).
 
-mode = 
+mode = idquaternion
 
 %%
 % The definition of colors for certain orientations is carried out similarly as 

help/doc/UsersGuide/EBSDAnalysis/GrainReconstruction.m

@@ -331,80 +331,3 @@
 % stop overide mode
 hold off
 
-%% ------------------------------------------------------
-%% this has to be reworked 
-
-%% Correcting poor grains
-% Sometimes measurements belonging to grains with very few measurements can
-% be regarded as inaccurate. This time, we explicitely keep the not
-% indexed measurements by the flag |keepNotIndexed|
-
-mtexdata forsterite
-
-[grains,ebsd.grainId] = calcGrains(ebsd,'angle',5*degree);
-
-close all
-plot(grains)
-
-%%
-% The number of measurements per grain can be accessed by the command
-% <GrainSet.grainSize.html GrainSize>. Let us determine the number of
-% grains with less then 10 measurements
-
-nnz(grains.grainSize < 5)
-
-% or the percentage of those grains relative to the total number of grains
-100 * nnz(grains.grainSize < 10) / length(grains)
-
-%%
-% We see that almost 92 percent of all grains consist of less then ten
-% measurement points. Next, we compute the percentage of small grains for
-% the individuell phases
-
-p = 100*[nnz(grains('notIndexed').grainSize < 10); ...
-  nnz(grains('forsterite').grainSize < 10); ...
-  nnz(grains('enstatite').grainSize < 10); ...
-  nnz(grains('diopside').grainSize < 10)]./length(grains)
-
-%%
-% We see that almost all small grains are acually not indexed. In order to
-% allow filling in those holes we remove these small not indexed grains
-% completely from the data set
-
-condition = grains.grainSize >=10 | grains.phase > 0;
-
-grains(condition)
-
-%%
-% If we now perform grain reconstruction a second time these small holes
-% will be assigned to the neighbouring grains
-
-grains = calcGrains(ebsd(grains(condition)),'keepNotIndexed')
-
-plot(grains)
-
-%%
-% We see that all small unindexed regions has been filled. Another way for
-% correcting EBSD data is to filter them accoring to quality measures like
-% MAD or band contrast. Lets plot the band contrast of our measurements
-
-plot(ebsd,ebsd.bc)
-
-colorbar
-
-%%
-% We see that there is a rectangular region in top left corner which low
-% band contrast. In order to filter out all measurements with low band
-% contrast we can do
-
-condition = ebsd.bc > 80;
-
-plot(ebsd(condition))
-
-%%
-% Although this filtering has cleared out large regions. The grain
-% reconstruction algorithm works still well.
-
-grains = calcGrains(ebsd(condition))
-
-plot(grains)