%% Import Script for EBSD Data
%
% This script was automatically created by the import wizard. You should
% run the whoole script or parts of it in order to import your data. There
% is no problem in making any changes to this script.

%% Specify Crystal and Specimen Symmetries

% crystal symmetry
CS = {... 
  'notIndexed',...
  crystalSymmetry('6/mmm', [3.2 3.2 5.2], 'X||a', 'Y||b*', 'Z||c*', 'mineral', 'Magnesium', 'color', [0.53 0.81 0.98])};

% plotting convention
setMTEXpref('xAxisDirection','south');
setMTEXpref('zAxisDirection','outOfPlane');

%% Specify File Names

% path to files
pname = 'D:\Prisms_plasticity';

% which files to be imported
fname = [pname '\Scan1.ang'];

%% Import the Data

% create an EBSD variable containing the data
ebsd = EBSD.load(fname,CS,'interface','ang',...
  'convertEuler2SpatialReferenceFrame');

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%[grains,ebsd.grainId,ebsd_after.mis2mean] = calcGrains(ebsd,'angle',5*degree);
grains = calcGrains(ebsd);
%ebsd(grains(grains.grainSize<3))=[];
% %ebsd(ebsd.prop.ci<1)=[];
% [grains_after,ebsd_after.grainId]=calcGrains(ebsd_after,'angle',5*degree);
% grains_after=smooth(grains_after,5);
  %F = halfQuadraticFilter;
  %F.alpha=10;  
%  F = splineFilter; 
%  ebsd_Sub_filled = smooth(ebsd,F,'fill',grains);
%ebsd_after_Sub_filled = ebsd_after;
%[grains,ebsdSub_filled('indexed').grainId]=calcGrains(ebsdSub_filled('indexed')); 
%[grains_Sub_filled,ebsd_Sub_filled('indexed').grainId]=calcGrains(ebsd_Sub_filled('indexed'),'threshold',[10*degree 1*degree]);
%grains_Sub_filled = calcGrains(ebsd_Sub_filled('indexed'));
%grains_Sub_filled=smooth(grains_Sub_filled,5);
ebsd_Sub_filled = ebsd;
grains_Sub_filled = grains;
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%%%%%%%%%%%%%%%%%%%%%%%%%%%     IPF map   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% plotting convention for mapping
setMTEXpref('xAxisDirection','east');
setMTEXpref('zAxisDirection','intoPlane');
ipfKey=ipfHSVKey(ebsd_Sub_filled('Magnesium'));
ipfKey.inversePoleFigureDirection.z=1;
figure(5)
plot(ipfKey);

% plot the ebsd data
figure(1)
colorsZr_HCP_after=ipfKey.orientation2color(ebsd_Sub_filled('Magnesium').orientations);
plot(ebsd_Sub_filled('Magnesium'),colorsZr_HCP_after)
%plot(ebsdSub_filled('Zr_HCP'),ebsdSub_filled('Zr_HCP').orientations,'faceAlpha',0.5,'figSize','large')

% init override mode
hold on

% plot grain boundares
plot(grains_Sub_filled.boundary,'linewidth',1.5)

hold off


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V=grains_Sub_filled.V;
ori = min(V);
grains_Sub_filled.V = V-repmat(ori,size(grains_Sub_filled.V,1),1);
G = gmshGeo(grains_Sub_filled);
G=simplify(G);
max(grains_Sub_filled.V)
%tic
mesh(G,'mesh.msh','ElementType','HexOnly','GrainPrefix','','thickness',1);
%mesh(G,'mesh.msh','ElementType','HexOnly','ElementSize',1.0,'GrainPrefix','','thickness',1);
%toc
exportGrainProps(G,'orientations_Ti2.txt','PRISMS')