%% Grain Tutorial

%

%%

% The following script is a quick guide through the grain reconstruction

% capabilities of MTEX. It uses the same data set as in the corresponding

% publication

% <https://www.researchgate.net/publication/51806709_Grain_detection_from_2d_and_3d_EBSD_data-Specification_of_the_MTEX_algorithm

% Grain detection from 2d and 3d EBSD data>. Data courtesy of Daniel Rutte

% and Bret Hacker, Stanford.

mtexdata mylonite

% plot a phase map

plot(ebsd)

%%

% The phase map displays a multi-phase rock specimen with phases such as

% Andesine, Quartz, Biotite, and Orthoclase. We will now focus on a smaller

% rectangular region of interest defined by the coordinates |[xmin, ymin,

% xmax - xmin, ymax - ymin]|.

region = [19000 1500 4000 1500];

% overlay the selected region on the phase map

rectangle('position',region,'edgecolor','k','linewidth',2)

%%

% Now copy the EBSD data within the selected rectangle to a new variable

ebsd_region = ebsd(inpolygon(ebsd,region))

%% Grain Reconstruction

% Next we reconstruct the grains and grain boundaries in the region of

% interest, using a 15 degree orientation change threshold.

grains = calcGrains(ebsd_region,'angle',15*degree)

% plot a phase map of the region of interest

plot(ebsd_region)

% overlay the grain boundaries

hold on

plot(grains.boundary,'color','k','linewidth',1.5)

hold off

%%

% We may also visualize the different quartz orientations together with the

% grain boundaries.

% plot a phase map of three of the phases based on the grains data

plot(grains({'Andesina','Biotite','Orthoclase'}),'FaceAlpha',0.4)

hold on

% add the quartz orientations as ipf map based on EBSD data

plot(ebsd_region('Quartz'),ebsd_region('Quartz').orientations)

% plot grain boundaries so that those in the Quartz are shown

plot(grains.boundary,'color','black');

legend off

hold off

%%

% In this visualization most phases are displayed in uniform colors, while

% Quartz is colored according to the ipf color key

close all

ipfKey = ipfColorKey(ebsd_region('Quartz'));

plot(ipfKey)

%%

% Alternatively, we can display each quartz grain according to its mean

% orientation.

plot(grains({'Andesina','Biotite','Orthoclase'}),'FaceAlpha',0.4)

hold on

plot(grains('Quartz'),grains('Quartz').meanOrientation)

legend off

%% Highlight specific boundaries

% We can create a phase map with certain grain boundaries highlighted. In

% this phase map, we highlight grain boundaries where neighboring grains of

% Andesine and Orthoclase exhibit a misorientation with a rotational axis

% close to the c-axis.

close all

% copy all boundaries between Andesina, Orthoclase to a new variable

AOboundary = grains.boundary('Andesina','Orthoclase');

% copy the misorientation angle of this boundary in radians to a new variable.

angle = AOboundary.misorientation.angle;

plot(grains,'FaceAlpha',0.4)

hold on

% highlight boundaries where the angle between the Andesina and Orthoclase phase is over 160 degrees

plot(AOboundary(angle>160*degree),'linewidth',2,'linecolor','red')

hold off

%%

% We can also represent the angular misorientation data between these two

% phases as a histogram.

figure;histogram(angle./degree)

xlabel('angle in degrees of boundary segment')

ylabel('count of boundary segments')

title('angular relationships between Andesina and Orthoclase')