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How to delete/alphadata values of 3d data outside polygon without change the dimensions of data

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We can delete the values of matrix outside polygon as
data = 12*17*6
x,y,S.X and S.Y are belongs to polygon
isin = inpolygon(X,Y,S.X,S.Y);
data(~isin) = [ ]
but it changes the dimension of data from 3d to single column
Secondly we can also use alphadata for 2d data easily as
imagesc(2ddata) 'AlphaData',~isin(2ddata))
1) How we can use the AlphaData for 3d data?
2) How we can delete values of 3d data outside polygon by keeping the data in same dimension

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