source: trunk/src/phys_ima.m @ 1078

Last change on this file since 1078 was 1078, checked in by sommeria, 8 months ago

various updates

File size: 4.2 KB
Line 
1
2% phys_ima: transform several images in phys coordinates on a common pixel grid
3%------------------------------------------------------------------------
4% OUTPUT:
5% A_out: cell array of oitput images corresponding to the transform of the input images
6% Rangx, Rangy; vectors with two elements defining the phys positions of first and last pixels in each direction
7%  (the same for all the ouput images)
8%
9% INPUT: 
10% A: cell array of input images
11% XmlData: cell array of structures defining the calibration parameters for each image
12% ZIndex: index of the reference plane used to define the phys position in 3D
13
14function [A_out,Rangx,Rangy]=phys_ima(A,XmlData,ZIndex)
15xcorner=[];
16ycorner=[];
17npx=[];
18npy=[];
19dx=ones(1,numel(A));
20dy=ones(1,numel(A));
21if isstruct(XmlData)
22    XmlData={XmlData};
23end
24
25for icell=1:numel(A)
26    siz=size(A{icell});
27    npx=[npx siz(2)];
28    npy=[npy siz(1)];
29    Calib=XmlData{icell}.GeometryCalib;
30    coord_x=[0.5 siz(2)-0.5];
31    coord_y=[0.5 siz(1)-0.5];
32    x_edge=[linspace(coord_x(1),coord_x(end),npx(icell)) coord_x(end)*ones(1,npy(icell))...
33        linspace(coord_x(end),coord_x(1),npx(icell)) coord_x(1)*ones(1,npy(icell))];%x coordinates of the image edge(four sides)
34    y_edge=[coord_y(1)*ones(1,npx(icell)) linspace(coord_y(1),coord_y(end),npy(icell))...
35        coord_y(end)*ones(1,npx(icell)) linspace(coord_y(end),coord_y(1),npy(icell))];%y coordinates of the image edge(four sides)
36    [xcorner_new,ycorner_new]=phys_XYZ(Calib,x_edge,y_edge,ZIndex);%corresponding physical coordinates
37    dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1);
38    dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1);
39    xcorner=[xcorner xcorner_new];
40    ycorner=[ycorner ycorner_new];
41end
42Rangx(1)=min(xcorner);
43Rangx(2)=max(xcorner);
44Rangy(2)=min(ycorner);
45Rangy(1)=max(ycorner);
46test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths
47
48npX=1+round((Rangx(2)-Rangx(1))/max(dx));% nbre of pixels in the new image (use the largest resolution max(dx) in the set of images)
49npY=1+round((Rangy(1)-Rangy(2))/max(dy));
50
51x=linspace(Rangx(1),Rangx(2),npX);
52y=linspace(Rangy(1),Rangy(2),npY);
53[X,Y]=meshgrid(x,y);%grid in physical coordinates
54A_out=cell(1,numel(A));
55
56for icell=1:length(A)
57    Calib=XmlData{icell}.GeometryCalib;
58    % rescaling of the image coordinates without change of the image array
59    if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib)
60        A_out{icell}=A{icell};%no transform
61        Rangx=[0.5 npx-0.5];%image coordiantes of corners
62        Rangy=[npy-0.5 0.5];
63        [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation
64        [~,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex);
65    else
66        % the image needs to be interpolated to the new coordinates
67        Z=0; %default
68        if isfield(Calib,'SliceCoord') %.Z= index of plane
69            SliceCoord=Calib.SliceCoord(ZIndex,:);
70            Z=SliceCoord(3);
71            if isfield(Calib, 'SliceAngle') && size(Calib.SliceAngle,1)>=ZIndex && ~isequal(Calib.SliceAngle(ZIndex,:),[0 0 0])
72                norm_plane=angle2normal(Calib.SliceAngle(ZIndex,:));
73                Z=Z-(norm_plane(1)*(X-SliceCoord(1))+norm_plane(2)*(Y-SliceCoord(2)))/norm_plane(3);
74            end
75        end
76        xima=0.5:npx(icell)-0.5;%image coordinates of corners
77        yima=npy(icell)-0.5:-1:0.5;
78        [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates
79        [XIMA,YIMA]=px_XYZ(XmlData{icell}.GeometryCalib,X,Y,Z);% image coordinates for each point in the real
80        testuint8=isa(A{icell},'uint8');
81        testuint16=isa(A{icell},'uint16');
82        if ismatrix(A{icell}) %(B/W images)
83            A_out{icell}=interp2(XIMA_init,YIMA_init,double(A{icell}),XIMA,YIMA);
84        elseif ndims(A{icell})==3
85            for icolor=1:size(A{icell},3)
86                A{icell}=double(A{icell});
87                A_out{icell}(:,:,icolor)=interp2(XIMA_init,YIMA_init,A{icell}(:,:,icolor),XIMA,YIMA);
88            end
89        end
90        if testuint8
91            A_out{icell}=uint8(A_out{icell});
92        end
93        if testuint16
94            A_out{icell}=uint16(A_out{icell});
95        end
96    end
97end
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