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rayCellGenerate.m
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153 lines (130 loc) · 7.54 KB
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function volImgRef_final = rayCellGenerate(volImgRef_final,raycellXind,raycellWidth,Params)
% function to generate ray cells
rayCellLength = Params.rayCellLength;
rayCell_variance = Params.rayCell_variance;
rayHeight = Params.rayHeight;
xGrid_all = Params.xGrid_all;
yGrid_all = Params.yGrid_all;
Thickness_all = Params.Thickness_all;
sizeImEnlarge = Params.sizeImEnlarge;
xGrid = Params.xGrid;
cellEndThick = Params.cellEndThick;
cellThick = Params.cellThick;
% raycellWidth(raycellWidth<-rayHeight | raycellWidth>sizeImEnlarge(3)+rayHeight) = [];
for i_raycolumn = raycellXind
% between first column and second column need a deviation
raycolumn_rand = 1/2*rayHeight;
s = 1;
vesselEndLoc = [];
vesselEndLoc(1) = -rayCellLength*rand(1);
while vesselEndLoc(s)<sizeImEnlarge(1)+rayCellLength
s = s+1;
temp = rayCellLength + rayCell_variance*randn(1);
if temp<rayCellLength/3
temp=2*rayCellLength;
else
if temp>2*rayCellLength
temp=2*rayCellLength;
end
end
vesselEndLoc(s) = vesselEndLoc(s-1)+temp;
end
vesselEndLoc = round(vesselEndLoc);
% vesselEndLoc = [1:rayCellLength:sizeImEnlarge(1)-rayCellLength/3]';
% vesselEndLoc = vesselEndLoc+round(rayCell_variance*rand(length(vesselEndLoc),1));
vesselEndLoc(vesselEndLoc>sizeImEnlarge(1)+rayCellLength/2) = [];
% vesselEndLoc1 = vesselEndLoc;
% for each column of ray cells,
% endRandom = round(rayCell_variance*1/4+rayCell_variance/2*rand(length(raycellWidth)));
for i_rayrow = 1:length(vesselEndLoc)-1
m2 = 0;
for j_slice = round(raycellWidth)
m2 = m2+1;
if mod(i_raycolumn,2) == 0
k = round(j_slice+round(raycolumn_rand));
else
k = j_slice;
end
t = round((max(1,k)+min(k+rayHeight,sizeImEnlarge(3)))/2);
if t >= 1 && t<sizeImEnlarge(3)-10
xGrid_t = reshape(xGrid_all(:,t),size(xGrid));
yGrid_t = reshape(yGrid_all(:,t),size(xGrid));
thickGrid_t = reshape(Thickness_all(:,t),size(xGrid));
yInterp1_C = spline(xGrid_t(:,i_raycolumn),yGrid_t(:,i_raycolumn),1:sizeImEnlarge(1))-1.5;
thickInterp_C = spline(xGrid_t(:,i_raycolumn),thickGrid_t(:,i_raycolumn),1:sizeImEnlarge(1));
yInterp2_C = spline(xGrid_t(:,i_raycolumn+1),yGrid_t(:,i_raycolumn+1),1:sizeImEnlarge(1))+1.5;
cell_center = [(1:length(yInterp2_C))',round(yInterp2_C(:)+yInterp1_C(:))/2,...
repmat((max(1,k)+min(k+rayHeight,sizeImEnlarge(3)))/2,length(yInterp2_C),1)];
cell_r = [(yInterp2_C(:)-yInterp1_C(:))/2,repmat((min(k+rayHeight,sizeImEnlarge(3))-max(1,k))/2,length(yInterp2_C),1)]+0.5;
vesselEndLoc_column = vesselEndLoc+round(mod(m2,2)*rayCellLength/2);
if vesselEndLoc_column(i_rayrow+1)<=sizeImEnlarge(1)-1 && vesselEndLoc_column(i_rayrow)>= 2
cell_neighPt = [vesselEndLoc_column(i_rayrow),vesselEndLoc_column(i_rayrow+1);
round(yInterp1_C(vesselEndLoc_column(i_rayrow))),...
round(yInterp2_C(vesselEndLoc_column(i_rayrow)));...
max(1,k),min(k+rayHeight,sizeImEnlarge(3))];
if i_rayrow == 1
i_valid = vesselEndLoc_column(i_rayrow)+cellEndThick:vesselEndLoc_column(i_rayrow+1)-cellEndThick/2;
else
if i_rayrow == length(vesselEndLoc)-1
i_valid = vesselEndLoc_column(i_rayrow)+cellEndThick/2-1:vesselEndLoc_column(i_rayrow+1)-cellEndThick/2;
else
i_valid = vesselEndLoc_column(i_rayrow)+cellEndThick/2-1:vesselEndLoc_column(i_rayrow+1)-cellEndThick/2;
end
end
for i = vesselEndLoc_column(i_rayrow)+1:vesselEndLoc_column(i_rayrow+1)
if j_slice == min(raycellWidth)
volImgRef_final(i,...
yInterp1_C(i):yInterp2_C(i),...
cell_center(i,3):cell_neighPt(3,2)) = 255;
else
if j_slice == max(raycellWidth)
volImgRef_final(i,...
yInterp1_C(i):yInterp2_C(i),...
cell_neighPt(3,1):cell_center(i,3)) = 255;
else
volImgRef_final(i,...
yInterp1_C(i):yInterp2_C(i),...
cell_neighPt(3,1):cell_neighPt(3,2)) = 255;
end
end
if find(round(i_valid) == i)
for j = cell_neighPt(2,1):cell_neighPt(2,2)
for s = cell_neighPt(3,1):cell_neighPt(3,2)
inner_elipse = (j-cell_center(i,2)).^2./(cell_r(i,1)-thickInterp_C(i))^2 ...
+ (s-cell_center(i,3)).^2./(cell_r(i,2)-thickInterp_C(i)).^2;
outer_elipse = (j-cell_center(i,2)).^2./(cell_r(i,1)).^2 ...
+ (s-cell_center(i,3)).^2./(cell_r(i,2)).^2;
if outer_elipse<1
volImgRef_final(i,j,s) = uint8(1./(1+exp(-(inner_elipse-1)/0.05))*255);
end
% if (j-cell_center(i,2))^2/(cell_r(i,1)-thickInterp_C(i))^2 ...
% + (s-cell_center(i,3))^2/(cell_r(i,2)-thickInterp_C(i))^2 <1
% volImgRef_final(i,j,s) = 0;
% else
% if ((j-cell_center(i,2))^2/(cell_r(i,1)-thickInterp_C(i)*2/3)^2 ...
% + (s-cell_center(i,3))^2/(cell_r(i,2)-thickInterp_C(i))^2) >=1 ...
% && ((j-cell_center(i,2))^2/(cell_r(i,1))^2 ...
% + (s-cell_center(i,3))^2/(cell_r(i,2))^2) <=1
% volImgRef_final(i,j,s) = 255;
% end
%
% end
end
end
% [j_grid,s_grid] = ndgrid(cell_neighPt(2,1):cell_neighPt(2,2),cell_neighPt(3,1):cell_neighPt(3,2));
%
% inner_elipse = (j_grid-cell_center(i,2)).^2./(cell_r(i,1)-thickInterp_C(i))^2 ...
% + (s_grid-cell_center(i,3)).^2./(cell_r(i,2)-thickInterp_C(i)).^2;
%
% outer_elipse = (j_grid-cell_center(i,2)).^2./(cell_r(i,1)).^2 ...
% + (s_grid-cell_center(i,3)).^2./(cell_r(i,2)).^2;
%
% volImgRef_final(i,cell_neighPt(2,1):cell_neighPt(2,2),cell_neighPt(3,1):cell_neighPt(3,2)) =...
% uint8(1./(1+exp(-(inner_elipse-1)/0.05))*255);
end
end
end
end
end
end
end