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@DorianDepriester
Last active September 22, 2022 17:57
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Determine the affine transform between two images or EBSD maps #mtexScript
function [M, U] = imageAligner(im0, varargin)
%%IMAGEALIGNER computes the affine transform between two images.
% [M, U]= IMAGEALIGNER(im0, im1) displays reference image im0 and deformed
% image im1 in two seperate figures, and the user is asked to locate points
% appearing in both images (control points). Then, the transform matrix M
% and the displacements U are given. Both images can be images as 2d array,
% EBSD data or of class grain2d.
%
% It is assumed that coordinates in reference image X are transformed into
% Y as follows:
% Y = M*X + U
%
% [...]=IMAGEALIGNER(im0,'field0',...) plots the field 'field0' for
% reference image. im0 must be of class EBSD or grain2d.
%
% [...]=IMAGEALIGNER(...,im1,'field1') plots the field 'field1' for
% deformed image. im1 must be of class EBSD or grain2d.
%
% Example:
% ebsd = EBSD.load('/Whatever/')
% sem = imread('SEM.tif');
% [M, U] = imageAligner(ebsd, 'orientations', sem);
% ebsd_aligned=affinetrans(ebsd,M,U); % Apply transform to EBSD data
%
% % Superimpose aligned EBSD and image
% plot(ebsd_aligned,ebsd_aligned.orientations,'micronbar','off')
% hold on
% im=imshow(sem);
% im.AlphaData = 0.7;
%
% See also affinetrans
%
%% Dialog box
txt1='Click alternatively on both images to specify the locations of control points. At least 3 points are required.';
txt2='Right click or press any key when it is done.';
uiwait(msgbox({txt1,txt2},'Locations of control points','help'));
%% Process input arguments
if ~ischar(varargin{1})
% imageAligner(data0, data1...
field0=[];
im1=varargin{1};
if nargin==2
%...)
field1=[];
else
%...,field1)
if ischar(varargin{2})
field1=varargin{2};
else
error('The 3th argument must be the name of the field to be displayed')
end
end
else
% imageAligner(array, field0, data1...
field0=varargin{1};
im1=varargin{2};
if nargin==3
%...)
field1=[];
else
%...,field1)
if ischar(varargin{3})
field1=varargin{3};
else
error('The 4th argument must be the name of the field to be displayed')
end
end
end
%% Open figure for transformed image
h1=figure('Name','Deformed data','NumberTitle','off');
if (isa(im1,'grain2d') || isa(im1,'EBSD'))
if isempty(field1)
plot(im1,'micronbar','off');
else
plot(im1, im1.(field1), 'micronbar', 'off');
end
else
imshow(im1)
end
hold on
s1=scatter([],[],[],'filled','MarkerEdgeColor',[0 0 0]);
%% Open figure for reference image
h0=figure('Name','Reference image','NumberTitle','off');
if (isa(im0,'grain2d') || isa(im0,'EBSD'))
if isempty(field0)
plot(im0,'micronbar','off');
else
plot(im0, im0.(field0), 'micronbar', 'off');
end
else
imshow(im0)
end
hold on
s0=scatter([],[],[],'filled','MarkerEdgeColor',[0 0 0]);
%% User specifies the control points
n=10;
Pts0=NaN(n,2);
Pts1=NaN(n,2);
i=1;
while true
figure(h0);
[x,y,b]=ginput(1);
if isempty(x) || b~=1
break
end
Pts0(i,:)=[x,y];
set(s0,'XData',Pts0(1:i,1),'YData',Pts0(1:i,2),'CData',lines(i));
figure(h1);
[x,y,b]=ginput(1);
if isempty(x) || b~=1
break
end
Pts1(i,:)=[x,y];
set(s1,'XData',Pts1(1:i,1),'YData',Pts1(1:i,2),'CData',lines(i));
i=i+1;
end
n=i-1;
if n<3
error('At least 3 control points must be defined.')
end
Pts0=Pts0(1:n,:);
Pts1=Pts1(1:n,:);
%% Compute M and U
% Centroids and local CSs
G0=mean(Pts0);
G1=mean(Pts1);
loc_coords_0=Pts0-repmat(G0,[n 1]);
loc_coords_1=Pts1-repmat(G1,[n 1]);
% Pseudo inverse
M=(loc_coords_0\loc_coords_1)';
U=G1'-M*G0';
end
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