[892] | 1 | |
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[849] | 2 | % phys_ima: transform several images in phys coordinates on a common pixel grid |
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| 3 | %------------------------------------------------------------------------ |
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| 4 | % OUTPUT: |
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| 5 | % A_out: cell array of oitput images corresponding to the transform of the input images |
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| 6 | % Rangx, Rangy; vectors with two elements defining the phys positions of first and last pixels in each direction |
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| 7 | % (the same for all the ouput images) |
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| 8 | % |
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| 9 | % INPUT: |
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| 10 | % A: cell array of input images |
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| 11 | % XmlData: cell array of structures defining the calibration parameters for each image |
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| 12 | % ZIndex: index of the reference plane used to define the phys position in 3D |
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| 13 | |
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| 14 | function [A_out,Rangx,Rangy]=phys_ima(A,XmlData,ZIndex) |
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| 15 | xcorner=[]; |
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| 16 | ycorner=[]; |
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| 17 | npx=[]; |
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| 18 | npy=[]; |
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| 19 | dx=ones(1,numel(A)); |
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| 20 | dy=ones(1,numel(A)); |
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| 21 | if isstruct(XmlData) |
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| 22 | XmlData={XmlData}; |
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| 23 | end |
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| 24 | for icell=1:numel(A) |
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| 25 | siz=size(A{icell}); |
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| 26 | npx=[npx siz(2)]; |
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| 27 | npy=[npy siz(1)]; |
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| 28 | Calib=XmlData{icell}.GeometryCalib; |
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| 29 | xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners |
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| 30 | yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5]; |
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| 31 | [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates |
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| 32 | dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1); |
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| 33 | dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1); |
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| 34 | xcorner=[xcorner xcorner_new]; |
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| 35 | ycorner=[ycorner ycorner_new]; |
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| 36 | end |
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| 37 | Rangx(1)=min(xcorner); |
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| 38 | Rangx(2)=max(xcorner); |
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| 39 | Rangy(2)=min(ycorner); |
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| 40 | Rangy(1)=max(ycorner); |
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| 41 | test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths |
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[922] | 42 | % npX=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) |
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| 43 | % npY=1+round((Rangy(1)-Rangy(2))/min(dy)); |
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| 44 | |
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| 45 | npX=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) |
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| 46 | npY=1+round((Rangy(1)-Rangy(2))/max(dy)); |
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| 47 | |
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| 48 | |
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[849] | 49 | x=linspace(Rangx(1),Rangx(2),npX); |
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| 50 | y=linspace(Rangy(1),Rangy(2),npY); |
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| 51 | [X,Y]=meshgrid(x,y);%grid in physical coordiantes |
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| 52 | %vec_B=[]; |
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| 53 | A_out=cell(1,numel(A)); |
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| 54 | for icell=1:length(A) |
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| 55 | Calib=XmlData{icell}.GeometryCalib; |
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| 56 | % rescaling of the image coordinates without change of the image array |
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| 57 | if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib) |
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| 58 | A_out{icell}=A{icell};%no transform |
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| 59 | Rangx=[0.5 npx-0.5];%image coordiantes of corners |
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| 60 | Rangy=[npy-0.5 0.5]; |
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| 61 | [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation |
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| 62 | [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex); |
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| 63 | else |
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| 64 | % the image needs to be interpolated to the new coordinates |
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| 65 | zphys=0; %default |
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| 66 | if isfield(Calib,'SliceCoord') %.Z= index of plane |
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| 67 | SliceCoord=Calib.SliceCoord(ZIndex,:); |
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| 68 | zphys=SliceCoord(3); %to generalize for non-parallel planes |
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[970] | 69 | |
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| 70 | % if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0]) |
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| 71 | % om=norm(Calib.SliceAngle);%norm of rotation angle in radians |
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| 72 | % OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis |
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| 73 | % cos_om=cos(pi*om/180); |
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| 74 | % sin_om=sin(pi*om/180); |
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| 75 | % pos=[xy(1,1) xy(1,2) 0]; |
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| 76 | % pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis; |
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| 77 | % end |
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| 78 | |
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| 79 | |
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[892] | 80 | % if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') |
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| 81 | % H=Calib.InterfaceCoord(3); |
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| 82 | % if H>zphys |
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| 83 | % zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object) |
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| 84 | % end |
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| 85 | % end |
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[849] | 86 | end |
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[922] | 87 | xima=0.5:npx(icell)-0.5;%image coordinates of corners |
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| 88 | yima=npy(icell)-0.5:-1:0.5; |
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[849] | 89 | [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates |
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| 90 | [XIMA,YIMA]=px_XYZ(XmlData{icell}.GeometryCalib,X,Y,zphys);% image coordinates for each point in the real |
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| 91 | testuint8=isa(A{icell},'uint8'); |
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| 92 | testuint16=isa(A{icell},'uint16'); |
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| 93 | if ndims(A{icell})==2 %(B/W images) |
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| 94 | A_out{icell}=interp2(XIMA_init,YIMA_init,double(A{icell}),XIMA,YIMA); |
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| 95 | elseif ndims(A{icell})==3 |
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| 96 | for icolor=1:size(A{icell},3) |
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| 97 | A{icell}=double(A{icell}); |
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| 98 | A_out{icell}(:,:,icolor)=interp2(XIMA_init,YIMA_init,A{icell}(:,:,icolor),XIMA,YIMA); |
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| 99 | end |
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| 100 | end |
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| 101 | if testuint8 |
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| 102 | A_out{icell}=uint8(A_out{icell}); |
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| 103 | end |
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| 104 | if testuint16 |
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| 105 | A_out{icell}=uint16(A_out{icell}); |
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| 106 | end |
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| 107 | end |
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| 108 | end |
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