source: trunk/src/phys_ima.m @ 849

Last change on this file since 849 was 849, checked in by sommeria, 6 years ago

phys ima added again

File size: 3.8 KB
Line 
1% phys_ima: transform several images in phys coordinates on a common pixel grid
2%------------------------------------------------------------------------
3% OUTPUT:
4% A_out: cell array of oitput images corresponding to the transform of the input images
5% Rangx, Rangy; vectors with two elements defining the phys positions of first and last pixels in each direction
6%  (the same for all the ouput images)
7%
8% INPUT: 
9% A: cell array of input images
10% XmlData: cell array of structures defining the calibration parameters for each image
11% ZIndex: index of the reference plane used to define the phys position in 3D
12
13function [A_out,Rangx,Rangy]=phys_ima(A,XmlData,ZIndex)
14xcorner=[];
15ycorner=[];
16npx=[];
17npy=[];
18dx=ones(1,numel(A));
19dy=ones(1,numel(A));
20if isstruct(XmlData)
21    XmlData={XmlData};
22end
23for icell=1:numel(A)
24    siz=size(A{icell});
25    npx=[npx siz(2)];
26    npy=[npy siz(1)];
27    Calib=XmlData{icell}.GeometryCalib;
28    xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners
29    yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
30    [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates
31    dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1);
32    dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1);
33    xcorner=[xcorner xcorner_new];
34    ycorner=[ycorner ycorner_new];
35end
36Rangx(1)=min(xcorner);
37Rangx(2)=max(xcorner);
38Rangy(2)=min(ycorner);
39Rangy(1)=max(ycorner);
40test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths
41npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images)
42npY=1+round((Rangy(1)-Rangy(2))/min(dy));
43x=linspace(Rangx(1),Rangx(2),npX);
44y=linspace(Rangy(1),Rangy(2),npY);
45[X,Y]=meshgrid(x,y);%grid in physical coordiantes
46%vec_B=[];
47A_out=cell(1,numel(A));
48for icell=1:length(A)
49    Calib=XmlData{icell}.GeometryCalib;
50    % rescaling of the image coordinates without change of the image array
51    if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib)
52        A_out{icell}=A{icell};%no transform
53        Rangx=[0.5 npx-0.5];%image coordiantes of corners
54        Rangy=[npy-0.5 0.5];
55        [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation
56        [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex);
57    else         
58        % the image needs to be interpolated to the new coordinates
59        zphys=0; %default
60        if isfield(Calib,'SliceCoord') %.Z= index of plane
61           SliceCoord=Calib.SliceCoord(ZIndex,:);
62           zphys=SliceCoord(3); %to generalize for non-parallel planes
63           if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex')
64                H=Calib.InterfaceCoord(3);
65                if H>zphys
66                    zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object)
67                end
68           end
69        end
70        xima=0.5:npx-0.5;%image coordinates of corners
71        yima=npy-0.5:-1:0.5;
72        [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates
73        [XIMA,YIMA]=px_XYZ(XmlData{icell}.GeometryCalib,X,Y,zphys);% image coordinates for each point in the real
74        testuint8=isa(A{icell},'uint8');
75        testuint16=isa(A{icell},'uint16');
76        if ndims(A{icell})==2 %(B/W images)
77        A_out{icell}=interp2(XIMA_init,YIMA_init,double(A{icell}),XIMA,YIMA);
78         elseif ndims(A{icell})==3     
79             for icolor=1:size(A{icell},3)
80                 A{icell}=double(A{icell});
81                 A_out{icell}(:,:,icolor)=interp2(XIMA_init,YIMA_init,A{icell}(:,:,icolor),XIMA,YIMA);
82             end
83         end
84        if testuint8
85            A_out{icell}=uint8(A_out{icell});
86        end
87        if testuint16
88            A_out{icell}=uint16(A_out{icell});
89        end     
90    end
91end
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