Get in touch with grains.
So far grains can be exclusively computed from EBSD data using the command calcGrains. In order to demonstrate grain reconstruction we import some EBSD data
mtexdata forsterite plotx2east % plot the Forsterite phase colorized according to orientation plot(ebsd('fo'),ebsd('fo').orientations)
When reconstructing grain there are two basic ways how to deal with not indexed measurements. The simplest way is to keep the not indexed pixels separately, i.e., do not assign them to any indexed grain.
[grains, ebsd.grainId] = calcGrains(ebsd,'angle',5*degree)
grains = grain2d Phase Grains Pixels Mineral Symmetry Crystal reference frame 0 16334 58485 notIndexed 1 4331 152345 Forsterite mmm 2 1866 26058 Enstatite mmm 3 2012 9064 Diopside 12/m1 Xa*, Yb*, Zc boundary segments: 148741 triple points: 12065 Properties: GOS, meanRotation ebsd = EBSD Phase Orientations Mineral Color Symmetry Crystal reference frame 0 58485 (24%) notIndexed 1 152345 (62%) Forsterite light blue mmm 2 26058 (11%) Enstatite light green mmm 3 9064 (3.7%) Diopside light red 12/m1 Xa*, Yb*, Zc Properties: bands, bc, bs, error, mad, x, y, grainId Scan unit : um
We observe that there are not only grains of specific phases but also not indexed grains. Let's add the grain boundaries to the previous plot.
hold on plot(grains.boundary) hold off
The resulting grains contain a lot of holes and onepixel grains. The second way is to assign not indexed pixels to surrounding grains. In MTEX this is done if the not indexed data are removed from the measurements, i.e.
ebsd = ebsd('indexed') % this removes all not indexed data [grains, ebsd.grainId] = calcGrains(ebsd,'angle',5*degree)
ebsd = EBSD Phase Orientations Mineral Color Symmetry Crystal reference frame 1 152345 (81%) Forsterite light blue mmm 2 26058 (14%) Enstatite light green mmm 3 9064 (4.8%) Diopside light red 12/m1 Xa*, Yb*, Zc Properties: bands, bc, bs, error, mad, x, y, grainId Scan unit : um grains = grain2d Phase Grains Pixels Mineral Symmetry Crystal reference frame 1 1256 152345 Forsterite mmm 2 518 26058 Enstatite mmm 3 1526 9064 Diopside 12/m1 Xa*, Yb*, Zc boundary segments: 45832 triple points: 3863 Properties: GOS, meanRotation ebsd = EBSD Phase Orientations Mineral Color Symmetry Crystal reference frame 1 152345 (81%) Forsterite light blue mmm 2 26058 (14%) Enstatite light green mmm 3 9064 (4.8%) Diopside light red 12/m1 Xa*, Yb*, Zc Properties: bands, bc, bs, error, mad, x, y, grainId Scan unit : um
Now, there are no not indexed grains computed. Let's visualize the result
% plot the orientation data of the Forsterite phase plot(ebsd('fo'),ebsd('fo').orientations) % plot the grain boundary on top of it hold on plot(grains.boundary) hold off
A more detailed discussion on grain reconstruction in MTEX can be found here
Due to the measurement grid, the grain boundaries often show a typical staircase effect. This effect can be reduced by smoothing the grain boundaries. Using the command smooth.
% smooth the grains grains = smooth(grains); % plot the orientation data of the Forsterite phase plot(ebsd('fo'),ebsd('fo').orientations) % plot the grain boundary on top of it hold on plot(grains.boundary) hold off
Grains are stored as a long list of several properties. Please find below a table of most of the properties that are stored or can be computed for grains
grain area in square grains.scanUnit 

grain length / grain width 

list of boundary segments 

number of boundary segments 

area difference between grain and its convex hull 

x,y coordinates of the barycenter of the grain 

grains.CS 
crystal symmetry (single phase only) 
diameter in grains.scanUnit 

the perimeter of the fitted ellipse 

the radius of the fitted ellipse 

grains.GOS 
grain orientation spread 
grains.grainSize 
number of measurements per grain 
check for inclusions 

grains.id 
grain id 
list of inner boundary segments 

grains.meanOrientation 
meanOrientation (single phase only) 
grains.mineral 
mineral name (single phase only) 
number and ids of neighboring grains 

grains.phase 
phase identifier 
perimeter in grains.scanUnit 

length and width of the fitted ellipse 

quotient perimeter / perimeter of the fitted ellipse 

list of triple points 

grains.x 
x coordinates of the vertices 
grains.y 
y coordinates of the vertices 
Those grain properties can be used for colorization. E.g. we may colorize grains according to their area.
plot(grains,grains.area)
or a little bit more advanced according to the log quotient between grain size and boundary size.
plot(grains,log(grains.grainSize ./ grains.boundarySize)) mtexColorbar
Note that some properties are available for single phase lists of grains, e.g.
% colorize the Forsterite Phase according to its mean orientation plot(grains('Fo'),grains('Fo').meanOrientation)
I'm going to colorize the orientation data with the standard MTEX colorkey. To view the colorkey do: oM = ipdfHSVOrientationMapping(ori_variable_name) plot(oM)
As with any list in MTEX, one can single out specific grains by conditions using the syntax
% this gives all grains with more the 1000 pixels largeGrains = grains(grains.grainSize > 1000) hold on % mark only large Forsterite grains plot(largeGrains('Fo').boundary,'linewidth',2,'linecolor','k') hold off
largeGrains = grain2d Phase Grains Pixels Mineral Symmetry Crystal reference frame 1 37 58902 Forsterite mmm 2 1 1038 Enstatite mmm boundary segments: 10886 triple points: 816 Properties: GOS, meanRotation
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